Targeting Magnaporthe oryzae effector MoErs1 and host papain-like protease OsRD21 interaction to combat rice blast.

Effector proteins secreted by plant pathogenic fungi are important artilleries against host immunity, but there is no precedent of such effectors being explored as antifungal targets. Here we demonstrate that MoErs1, a species-specific effector protein secreted by the rice blast fungus Magnaporthe oryzae, inhibits the function of rice papain-like cysteine protease OsRD21 involved in rice immunity. Disrupting MoErs1-OsRD21 interaction effectively controls rice blast. In addition, we show that FY21001, a structure-function-based designer compound, specifically binds to and inhibits MoErs1 function. FY21001 significantly and effectively controls rice blast in field tests. Our study revealed a novel concept of targeting pathogen-specific effector proteins to prevent and manage crop diseases.

BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases.

Prime editing allows precise installation of any single base substitution and small insertions and deletions without requiring homologous recombination or double-strand DNA breaks in eukaryotic cells. However, the applications in bacteria are hindered and the underlying mechanisms that impede efficient prime editing remain enigmatic. Here, we report the determination of vital cellular factors that affect prime editing in bacteria. Genetic screening of 129 Escherichia coli transposon mutants identified sbcB, a 3'→5' DNA exonuclease, as a key genetic determinant in impeding prime editing in E. coli, combinational deletions of which with two additional 3'→5' DNA exonucleases, xseA and exoX, drastically enhanced the prime editing efficiency by up to 100-fold. Efficient prime editing in wild-type E. coli can be achieved by simultaneously inhibiting the DNA exonucleases via CRISPRi. Our results pave the way for versatile applications of prime editing for bacterial genome engineering.

Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we use single-cell RNA sequencing (scRNA-seq) to examine immune cells in patient and control cohorts. Postexertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. To detect changes coincident with PEM, we applied scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients display classical monocyte dysregulation suggestive of inappropriate differentiation and migration to tissue. We identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlates with disease severity. Comparing the transcriptome at baseline and postexercise challenge, we discover patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation in platelets.

Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System.

CRISPR-Cas9 systems have been widely harnessed for diverse genome editing applications because of their ease of use and high efficiency. However, the large molecular sizes and strict PAM requirements of commonly used CRISPR-Cas9 systems restrict their broad applications in therapeutics. Here, we report the molecular basis and genome editing applications of a novel compact type II-A Eubacterium ventriosum CRISPR-Cas9 system (EvCas9) with 1107 residues and distinct 5'-NNGDGN-3' (where D represents A, T, or G) PAM specificity. We determine the cryo-EM structure of EvCas9 in a complex with an sgRNA and a target DNA, revealing the detailed PAM recognition and sgRNA and target DNA association mechanisms. Additionally, we demonstrate the robust genome editing capacity of EvCas9 in bacteria and human cells with superior fidelity compared to SaCas9 and SpCas9, and we engineer it to be efficient base editors by fusing a cytidine or adenosine deaminase. Collectively, our results facilitate further understanding of CRISPR-Cas9 working mechanisms and expand the compact CRISPR-Cas9 toolbox.

A KDPG sensor RccR governs Pseudomonas aeruginosa carbon metabolism and aminoglycoside antibiotic tolerance.

Pseudomonas aeruginosa harbors sophisticated transcription factor (TF) networks to coordinately regulate cellular metabolic states for rapidly adapting to changing environments. The extraordinary capacity in fine-tuning the metabolic states enables its success in tolerance to antibiotics and evading host immune defenses. However, the linkage among transcriptional regulation, metabolic states and antibiotic tolerance in P. aeruginosa remains largely unclear. By screening the P. aeruginosa TF mutant library constructed by CRISPR/Cas12k-guided transposase, we identify that rccR (PA5438) is a major genetic determinant in aminoglycoside antibiotic tolerance, the deletion of which substantially enhances bacterial tolerance. We further reveal the inhibitory roles of RccR in pyruvate metabolism (aceE/F) and glyoxylate shunt pathway (aceA and glcB), and overexpression of aceA or glcB enhances bacterial tolerance. Moreover, we identify that 2-keto-3-deoxy-6-phosphogluconate (KDPG) is a signal molecule that directly binds to RccR. Structural analysis of the RccR/KDPG complex reveals the detailed interactions. Substitution of the key residue R152, K270 or R277 with alanine abolishes KDPG sensing by RccR and impairs bacterial growth with glycerol or glucose as the sole carbon source. Collectively, our study unveils the connection between aminoglycoside antibiotic tolerance and RccR-mediated central carbon metabolism regulation in P. aeruginosa, and elucidates the KDPG-sensing mechanism by RccR.

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.

The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.

Translation of interacting cavitation bubble in a plane acoustic field.

In a plane acoustic field, a model involving the radial and translational motions of bubble is derived, which is used to numerically investigate the translation of two interacting spherical cavitation bubbles. For the smaller initial distance between bubble centers, we investigate the dynamics of two bubbles, and find that they could come into contact but the velocities of closing to each other are different when the equilibrium radius is different. The results show that when the wavelength of plane acoustic field is much larger than the initial distance, the bubbles are approximately pulsating in phase. Moreover, the velocity of contact process of two bubbles can be changed by adjusting the parameters of plane acoustic field. For increasing in the initial distance, the bubbles would present two translation motions: close to each other for the pulsating in phase and away from each other for the pulsating out of phase, which could be verified by calculating the secondary Bjerknes force. Meanwhile, the larger the initial distance, the smaller the secondary Bjerknes force value is. Understanding the translation of bubble is of great significance for helpful explaining formation of streamer structures in ultrasonic cavitation.

Identification of plant cadmium resistance gene family in Brassica napus and functional analysis of BnPCR10.1 involved in cadmium and copper tolerance.

The plant cadmium resistance (PCR) family proteins play important roles in maintaining metal homeostasis and detoxification. However, few functional PCR genes have been well-characterized in plants. In this study, we identified and cloned 26 BnPCR genes from the rapeseed (Brassica napus) genome. They were divided into four groups (I-IV) based on their phylogenetic relationship. Yeast functional complementation experiments showed that BnPCRs can transport copper (Cu) and cadmium (Cd) in yeast. The expression levels of the BnPCRs were variable among different organs. Moreover, most of the genes were induced by Cu2+ and Cd2+ stress. Among these genes, BnPCR10.1 was highly expressed in various organs and induced by Cu2+ and Cd2+. Therefore, we studied the function of BnPCR10.1 in more detail. BnPCR10.1 was localized to the plasma membrane (PM), and expression in yeast enhanced yeast cells to export Cu and Cd. Furthermore, overexpression of BnPCR10.1 transgenic lines pro35S::BnPCR10.1;athma5 had lower concentration of Cu in roots than athma5 mutants. In addition, transgenic plants pro35S::BnPCR10.1;atpdr8 had lower concentration of Cd in shoots and roots than atpdr8 mutants. Net Cu2+ and Cd2+ efflux assay showed that there was decreased absorption of Cu2+ and Cd2+ in the transgenic Arabidopsis elongation zone of roots than in athma5 and atpdr8 mutants, respectively. These results provide new information on BnPCRs and their roles in response to heavy metals and reveal the mechanism used by BnPCR10.1 to detoxify Cu and Cd. Our findings facilitate a theoretical basis for the genetic improvement of Cu-Cd tolerance in rapeseed.

Cas12n nucleases, early evolutionary intermediates of type V CRISPR, comprise a distinct family of miniature genome editors.

Type V CRISPR-associated systems (Cas)12 family nucleases are considered to have evolved from transposon-associated TnpB, and several of these nucleases have been engineered as versatile genome editors. Despite the conserved RNA-guided DNA-cleaving functionality, these Cas12 nucleases differ markedly from the currently identified ancestor TnpB in aspects such as guide RNA origination, effector complex composition, and protospacer adjacent motif (PAM) specificity, suggesting the presence of earlier evolutionary intermediates that could be mined to develop advanced genome manipulation biotechnologies. Using evolutionary and biochemical analyses, we identify that the miniature type V-U4 nuclease (referred to as Cas12n, 400-700 amino acids) is likely the earliest evolutionary intermediate between TnpB and large type V CRISPR systems. We demonstrate that with the exception of CRISPR array emergence, CRISPR-Cas12n shares several similar characteristics with TnpB-ωRNA, including a miniature and likely monomeric nuclease for DNA targeting, origination of guide RNA from nuclease coding sequence, and generation of a small sticky end following DNA cleavage. Cas12n nucleases recognize a unique 5'-AAN PAM sequence, of which the A nucleotide at the -2 position is also required for TnpB. Moreover, we demonstrate the robust genome-editing capacity of Cas12n in bacteria and engineer a highly efficient CRISPR-Cas12n (termed Cas12Pro) with up to 80% indel efficiency in human cells. The engineered Cas12Pro enables base editing in human cells. Our results further expand the understanding regarding type V CRISPR evolutionary mechanisms and enrich the miniature CRISPR toolbox for therapeutic applications.

Rapid and Ultrasensitive Detection of Plasmodium spp. Parasites via the RPA-CRISPR/Cas12a Platform.

Microscopic examination of thick and thin blood smears stained with Giemsa dye is considered the primary diagnostic tool for the confirmation and management of suspected clinical malaria. However, detecting gametocytes is relatively insensitive, particularly in asymptomatic individuals with low-density Plasmodium infections. To complement existing diagnostic methods, a rapid and ultrasensitive point-of-care testing (POCT) platform for malaria detection is urgently needed and necessary. A platform based on recombinase polymerase amplification (RPA) followed by CRISPR/Cas12a (referred to as RPA-CRISPR/Cas12a) was developed and optimized for the determination of Plasmodium spp. parasites, particularly Plasmodium falciparum, using a fluorescence-based assay (FBDA), lateral flow test strips (LFTS), or naked eye observation (NEO). Then, the established platform was assessed with clinical malaria isolates. Under optimal conditions, the detection threshold was 1 copy/µL for the plasmid, and the limit of detection was 3.11-7.27 parasites/µL for dried blood spots. There was no cross-reactivity against blood-borne pathogens. For the accuracies of RPA-CRISPR/Cas12a, Plasmodium spp. and P. falciparum testing were 98.68 and 94.74%, respectively. The method was consistent with nested PCR results and superior to the qPCR results. RPA-CRISPR/Cas12a is a rapid, ultrasensitive, and reliable platform for malaria diagnosis. The platform requires no or minimal instrumentation for nucleic acid amplification reactions and can be read with the naked eye. Compared with similar diagnostic methods, this platform improves the reaction speed while reducing detection requirements. Therefore, this platform has the potential to become a true POCT for malaria parasites.

A novel fluorescence probe for the recognition of Cd2+ and its application.

A facile fluorescence probe BQBH was synthesized and investigated on its spectrum property. The result showed that the BQBH had high sensitivity and selectivity for Cd2+ with lowest detection determined as 0.14 µM by fluorescence response. The 1: 1 binding ratio between BQBH and Cd2+ was determined by Job's plot, and the binding details were further confirmed by 1H NMR titration, FT-IR spectrum and HRMS analysis. The applications including on test paper, smart phone and cell image were all also investigated.

A FIN-LDMOS with Bulk Electron Accumulation Effect.

A thin Silicon-On-Insulator (SOI) LDMOS with ultralow Specific On-Resistance (Ron,sp) is proposed, and the physical mechanism is investigated by Sentaurus. It features a FIN gate and an extended superjunction trench gate to obtain a Bulk Electron Accumulation (BEA) effect. The BEA consists of two p-regions and two integrated back-to-back diodes, then the gate potential VGS is extended through the whole p-region. Additionally, the gate oxide Woxide is inserted between the extended superjunction trench gate and N-drift. In the on-state, the 3D electron channel is produced at the P-well by the FIN gate, and the high-density electron accumulation layer formed in the drift region surface provides an extremely low-resistance current path, which dramatically decreases the Ron,sp and eases the dependence of Ron,sp on the drift doping concentration (Ndrift). In the off-state, the two p-regions and N-drift deplete from each other through the gate oxide Woxide like the conventional SJ. Meanwhile, the Extended Drain (ED) increases the interface charge and reduces the Ron,sp. The 3D simulation results show that the BV and Ron,sp are 314 V and 1.84 mΩ∙cm-2, respectively. Consequently, the FOM is high, reaching up to 53.49 MW/cm2, which breaks through the silicon limit of the RESURF.

Technological achievements in regional economic development: An econometrics analysis based on DEA.

"Double circulation" is an important strategic choice under the development of the new situation. The transformation of university scientific and technological achievements and the coordinated development of regional economy are of great significance to the construction and development of the new paradigm. In this paper, DEA method is used to measure the transformation efficiency of scientific and technological achievements of universities in 31 provinces and autonomous regions (excluding Hong Kong, Macao and Taiwan), and the entropy weight-Topsis model is used to evaluate the quality of regional economic development. The comprehensive scores of the two systems are coupled and coordinated finally. It is found that the transformation efficiency of scientific and technological achievements of universities in 31 provinces and autonomous regions (excluding Hong Kong, Macao and Taiwan) is mostly DEA effective, and the transformation ability of scientific and technological achievements of universities is strong in the regions where university resources are concentrated and the economically developed regions, meanwhile there is a big gap between regions. The transformation ability of scientific and technological achievements in the central and western regions has a big room for improvement. The transformation level of scientific and technological achievements of universities in most provinces is still at a middle level of coordination with the level of regional economic development. In view of the above research conclusions, some countermeasures and suggestions are put forward in order to promote the transformation of scientific and technological achievements and regional economic development can be more coordinated.

m6 A-Dependent Modulation via IGF2BP3/MCM5/Notch Axis Promotes Partial EMT and LUAD Metastasis.

The importance of mRNA N6-methyladenosine (m6 A) modification during tumor metastasis is controversial as it plays distinct roles in different biological contexts. Moreover, how cancer cell plasticity is shaped by m6 A modification is interesting but remains uncharacterized. Here, this work shows that m6 A reader insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) is remarkably upregulated in metastatic lung adenocarcinoma (LUAD) and indicates worse prognosis of patients. Interestingly, IGF2BP3 induces partial epithelial-mesenchymal-transition (EMT) and confers LUAD cells plasticity to metastasize through m6 A-dependent overactivation of Notch signaling. Mechanistically, IGF2BP3 recognized m6 A-modified minichromosome maintenance complex component (MCM5) mRNAs to prolong stability of them, subsequently upregulating MCM5 protein, which competitively inhibits SIRT1-mediated deacetylation of Notch1 intracellular domain (NICD1), stabilizes NICD1 protein and contributes to m6 A-dependent IGF2BP3-mediated cellular plasticity. Notably, a tight correlation of the IGF2BP3/MCM5/Notch axis is evidenced in clinical LUAD specimens. Therefore, this study elucidates a critical role of m6 A modification on LUAD cell plasticity in fostering tumor metastasis via the above axis, providing potential targets for metastatic LUAD.

GaN nanowires prepared by Cu-assisted photoelectron-chemical etching.

A novel Cu-assisted photoelectron-chemical etching is proposed to fabricate GaN nanowires. The functional mechanism of assisted metals, etchant concentrations, and the addition of H2O2 was investigated based on theoretical analysis and experiments. The low-cost metal-assisted etchant (CuSO4) proved more favorable than the conventional noble one (AgNO3) for the preparation of GaN nanowires in this work. The formed Ag dendrite blocked the etching when adopting the Ag-assisted etchant, while the Cu-assisted one did not. Moreover, the etchant consisting of 0.01 M CuSO4 and 5 M HF was demonstrated to realize a relatively good surface morphology and fast etching rate. In addition, the common oxidant H2O2 introduced a quasi-stable configuration between the Cu deposition and dissolution, slowing down the formation of the GaN nanowires. The proposed Cu-assisted photoelectron-chemical etching with the advantages of low cost, room temperature, and controllability could offer a new way to fabricate GaN nano-devices.

Ethnicity Disparities in the Prevalence, Awareness, Treatment, and Control Rates of Hypertension in China.

Objectives: Previous studies reported that there were disparities in hypertension management among different ethnic groups, and this study aimed to systematically determine the prevalence, awareness, treatment, and control rates of hypertension in multiple Chinese ethnic groups. Methods: We searched Embase, PubMed, and Web of Science for articles up to 25 October, 2022. The pooled prevalence, awareness, treatment, and control rates of hypertension were estimated with 95% confidence intervals (CI). The heterogeneity of estimates among studies was assessed by the Cochran Q test and I 2 statistic. Meta-regression analyses were conducted to identify the factors influencing the heterogeneity of the pooled prevalence, awareness, treatment, and control rate of hypertension. Results: In total, 45 publications including 193,788 cases and 587,826 subjects were eligible for the analyses. The lowest prevalence was found in the Han group (27.0%), and the highest prevalence was in the Mongolian population (39.8%). The awareness rates ranged from 24.4% to 58.0% in the four ethnic groups. Both the highest treatment and control rates were found in the Mongolian population (50.6% and 16.0%, respectively), whereas the Yi group had the lowest control rate (8.0%). In addition, the study year, the mean age of subjects, mean body mass index of subjects, tobacco use (%), alcohol use (%), residence (urban%), and education (primary school%) had varied effects on heterogeneity. Conclusions: These findings highlight the disparities in prevalence, awareness, treatment, and control rates of hypertension in a different ethnic population of China, which could provide suggestions for making targeted prevention measures.

A Rapid Antimicrobial Resistance Diagnostic Platform for Staphylococcus aureus Using Recombinase Polymerase Amplification.

Antimicrobial resistance (AMR) has posed a global threat to public health. The Staphylococcus aureus strains have especially developed AMR to practically all antimicrobial medications. There is an unmet need for rapid and accurate detection of the S. aureus AMR. In this study, we developed two versions of recombinase polymerase amplification (RPA), the fluorescent signal monitoring and lateral flow dipstick, for detecting the clinically relevant AMR genes retained by S. aureus isolates and simultaneously identifying such isolates at the species level. The sensitivity and specificity were validated with clinical samples. Our results showed that this RPA tool was able to detect antibiotic resistance for all the 54 collected S. aureus isolates with high sensitivity, specificity, and accuracy (all higher than 92%). Moreover, results of the RPA tool are 100% consistent with that of PCR. In sum, we successfully developed a rapid and accurate AMR diagnostic platform for S. aureus. The RPA might be used as an effective diagnostic test in clinical microbiology laboratories to improve the design and application of antibiotic therapy. IMPORTANCE Staphylococcus aureus is a species of Staphylococcus and belongs to Gram-positive. Meanwhile, S. aureus remains one of the most common nosocomial and community-acquired infections, causing blood flow, skin, soft tissue, and lower respiratory tract infections. The identification of the particular nuc gene and the other eight genes of drug-resistant S. aureus can reliably and quickly diagnose the illness, allowing doctors to prescribe treatment regimens sooner. The detection target in this work is a particular gene of S. aureus, and a POCT is built to simultaneously recognize S. aureus and analyze genes representing four common antibiotic families. We developed and assessed a rapid and on-site diagnostic platform for the specific and sensitive detection of S. aureus. This method allows the determination of S. aureus infection and 10 different AMR genes representing four different families of antibiotics within 40 min. It was easily adaptable in low-resource circumstances and professional-lacking circumstances. It should be supported in overcoming the continuous difficulty of drug-resistant S. aureus infections, which is a shortage of diagnostic tools that can swiftly detect infectious bacteria and numerous antibiotic resistance indicators.

Translation of cavitation bubble near the different walls.

The interaction between spherical cavitation bubble and flat wall is transformed into that between the real bubble and imaging bubble by the method of images. Firstly, we investigate the dynamics of real bubble and matched, inversed or mis-matched imaging bubble driven by a small amplitude ultrasound, revealing the characteristics of the interaction between cavitation bubble and rigid, soft and impedance walls. Then, we emphatically study the dynamics of real bubble and mis-matched imaging bubble driven by a finite amplitude ultrasound, and the interaction characteristics between cavitation bubble and real impedance wall are revealed. The results show that the cavitation bubble is always close to the rigid wall and far away from the soft wall; For the impedance wall, whether the cavitation bubble is far away or close depends on the specific wall parameters. Moreover, the direction and magnitude of bubble's translation velocity can be changed by adjusting the driving parameters. Understanding the interaction between cavitation bubble and impedance wall is of great significance for efficient application of ultrasonic cavitation.

The effect of bulk viscosity on single bubble dynamics and sonoluminescence.

In our previous paper, we derived a new single bubble model including the effect of bulk viscosity. To confront it to experiments, single bubble dynamics was measured here in 30% (v/v) glycerol-water mixture under different acoustic amplitudes and compared to models including or not the effect of bulk viscosity. The results showed that calculated bubble dynamics were not significantly affected by the bulk viscosity within the experimental conditions used in this study. However, there was a noticeable delay for the first rebound when bulk viscosity was considered. The corresponding sonoluminescence intensities were collected and compared with theoretical predictions. The results did not allow to discriminate between the two models (one includes the effect of bulk viscosity, the other does not), confirming the negligible effect of bulk viscosity in this condition (30% (v/v) glycerol-water mixture). Due to the instability of a single bubble in higher viscosity solutions, we could not implement experiments that can discriminate between the two models.

Insights into the health status of the general population living near an electroplating industry zone: metal elevations and renal impairment.

A cross-sectional study was conducted in 2016 in Zhejiang Province, China, to evaluate the body burdens of metals and metalloids associated with renal dysfunction in populations living near electroplating industries. We recruited 236 subjects and performed physical examinations, determined the blood and urinary levels of arsenic (As), cadmium (Cd), chromium (Cr), manganese (Mn), nickel (Ni), lead (Pb), antimony (Sb), and selenium (Se) by an inductively coupled plasma mass spectrometer (ICP-MS), and measured three renal impairment biomarkers, namely nacetyl-ß-D-glucosaminidase (NAG), retinol-binding protein (RBP), and ß2-microglobulin (BMG). The proportion of abnormal nasal symptoms in the exposure group (10.1%) was much higher than in the control group (0; p < 0.05). The blood and urinary levels of As, Cd, and Se in the exposure group were significantly higher than those in the control group (p < 0.05). The blood levels of Mn and Pb, as well as the urinary levels of Cr and Ni, were significantly higher in the exposure group than in the control group (p < 0.05). The exposure group demonstrated higher levels of NAG, RBP, and BMG than the control group (0.51 vs. 0.14 mg/g creatinine, 12.79 vs. 9.26 IU/g creatinine, and 1.39 vs. 0.78 mg/g creatinine, respectively; p < 0.05). Urinary BMG was positively correlated with urinary Cd levels (r = 0.223, p < 0.05), while urinary RBP was correlated with blood Cd levels (r = 0.151, p < 0.05) and urinary Cd, Cr, Ni, and Se levels (r = 0.220, 0.303, 0.162, and 0.306, respectively; p < 0.05). In conclusion, our study indicated that a population living in the vicinity of electroplating industries had high body burdens of certain metals and metalloids associated with non-negligible renal dysfunction.