PE/PPE mutations in the transmission of Mycobacterium tuberculosis in China revealed by whole genome sequencing.

OBJECTIVE: This study aims to examine the impact of PE/PPE gene mutations on the transmission of Mycobacterium tuberculosis (M. tuberculosis) in China. METHODS: We collected the whole genome sequencing (WGS) data of 3202 M. tuberculosis isolates in China from 2007 to 2018 and investigated the clustering of strains from different lineages. To evaluate the potential role of PE/PPE gene mutations in the dissemination of the pathogen, we employed homoplastic analysis to detect homoplastic single nucleotide polymorphisms (SNPs) within these gene regions. Subsequently, logistic regression analysis was conducted to analyze the statistical association. RESULTS: Based on nationwide M. tuberculosis WGS data, it has been observed that the majority of the M. tuberculosis burden in China is caused by lineage 2 strains, followed by lineage 4. Lineage 2 exhibited a higher number of transmission clusters, totaling 446 clusters, of which 77 were cross-regional clusters. Conversely, there were only 52 transmission clusters in lineage 4, of which 9 were cross-regional clusters. In the analysis of lineage 2 isolates, regression results showed that 4 specific gene mutations, PE4 (position 190,394; c.46G > A), PE_PGRS10 (839,194; c.744 A > G), PE16 (1,607,005; c.620T > G) and PE_PGRS44 (2,921,883; c.333 C > A), were significantly associated with the transmission of M. tuberculosis. Mutations of PE_PGRS10 (839,334; c.884 A > G), PE_PGRS11 (847,613; c.1455G > C), PE_PGRS47 (3,054,724; c.811 A > G) and PPE66 (4,189,930; c.303G > C) exhibited significant associations with the cross-regional clusters. A total of 13 mutation positions showed a positive correlation with clustering size, indicating a positive association. For lineage 4 strains, no mutations were found to enhance transmission, but 2 mutation sites were identified as risk factors for cross-regional clusters. These included PE_PGRS4 (338,100; c.974 A > G) and PPE13 (976,897; c.1307 A > C). CONCLUSION: Our results indicate that some PE/PPE gene mutations can increase the risk of M. tuberculosis transmission, which might provide a basis for controlling the spread of tuberculosis.

Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans.

DHH/DHHA1 family proteins have been proposed to play critical roles in bacterial resistance to environmental stresses. Members of the most radioresistant bacteria genus, Deinococcus, possess two DHH/DHHA1 family proteins, RecJ and RecJ-like. While the functions of Deinococcus radiodurans RecJ (DrRecJ) in DNA damage resistance have been well characterized, the role and biochemical activities of D. radiodurans RecJ-like (DrRecJ-like) remain unclear. Phenotypic and transcriptomic analyses suggest that, beyond DNA repair, DrRecJ is implicated in cell growth and division. Additionally, DrRecJ-like not only affects stress response, cell growth, and division but also correlates with the folding/stability of intracellular proteins, as well as the formation and stability of cell membranes/walls. DrRecJ-like exhibits a preferred catalytic activity towards short single-stranded RNA/DNA oligos and c-di-AMP. In contrast, DrRecJ shows no activity against RNA and c-di-AMP. Moreover, a crystal structure of DrRecJ-like, with Mg2+ bound in an open conformation at a resolution of 1.97 Å, has been resolved. Subsequent mutational analysis was conducted to pinpoint the crucial residues essential for metal cation and substrate binding, along with the dimerization state, necessary for DrRecJ-like's function. This finding could potentially extend to all NrnA-like proteins, considering their conserved amino acid sequence and comparable dimerization forms.

Diagnosis of Nonalcoholic Fatty Liver Disease via a H2S-Responsive Bioluminescent Probe Combined with Firefly Luciferase mRNA Delivery.

The early detection of nonalcoholic fatty liver disease (NAFLD) through bioluminescent probes is of great significance. However, there remains a challenge to apply them in nontransgenic natural animals due to the lack of exogenous luciferase. To address this issue, we herein report a new strategy for in situ monitoring of endogenous hydrogen sulfide (H2S) in the liver of NAFLD mice by leveraging a H2S-responsive bioluminescent probe (H-Luc) combined with firefly luciferase (fLuc) mRNA delivery. The probe H-Luc was created by installing a H2S recognition moiety, 2,4-dinitrophenol, onto the luciferase substrate (d-luciferin), which is allowed to release cage-free d-luciferin in the presence of H2S via a nucleophilic aromatic substitution reaction. In the meantime, the intracellular luciferase was introduced by lipid nanoparticle (LNP)-mediated fLuc mRNA delivery, rendering it suitable for bioluminescence (BL) imaging in vitro and in vivo. Based on this luciferase-luciferin system, the endogenous H2S could be sensitively and selectively detected in living cells, showing a low limit of detection (LOD) value of 0.72 µM. More importantly, after systematic administration of fLuc mRNA-loaded LNPs in vivo, H-Luc was able to successfully monitor the endogenous H2S levels in the NAFLD mouse model for the first time, displaying a 28-fold higher bioluminescence intensity than that in the liver of normal mice. We believe that this strategy may shed new light on the diagnosis of inflammatory liver disease, further elucidating the roles of H2S.

Visualization of Endogenous Hypochlorite in Drug-Induced Liver Injury Mice via a Bioluminescent Probe Combined with Firefly Luciferase mRNA-Loaded Lipid Nanoparticles.

Drug-induced liver injury (DILI) is a common liver disease with a high rate of morbidity, and its pathogenesis is closely associated with the overproduction of highly reactive hypochlorite (ClO-) in the liver. However, bioluminescence imaging of endogenous hypochlorite in nontransgenic natural mice remains challenging. Herein, to address this issue, we report a strategy for imaging ClO- in living cells and DILI mice by harnessing a bioluminescent probe formylhydrazine luciferin (ClO-Luc) combined with firefly luciferase (fLuc) mRNA-loaded lipid nanoparticles (LNPs). LNPs could efficiently deliver fLuc mRNA into living cells and in vivo, expressing abundant luciferase in the cytoplasm in situ. In the presence of ClO-, probe ClO-Luc locked by formylhydrazine could release cage-free d-luciferin through oxidation and follow-up hydrolysis reactions, further allowing for bioluminescence imaging. Moreover, based on the luciferase-luciferin system, it was able to sensitively and selectively detect ClO- in vitro with a limit of detection of 0.59 µM and successfully monitor the endogenous hypochlorite generation in the DILI mouse model for the first time. We postulate that this work provides a new method to elucidate the roles of ClO- in related diseases via bioluminescence imaging.

Recent Advancements on Spin Engineering Strategies for Highly Efficient Electrocatalytic Oxygen Evolution Reactions.

Oxygen evolution reaction (OER) is a widely employed half-electrode reaction in oxygen electrochemistry, in applications such as hydrogen evolution, carbon dioxide reduction, ammonia synthesis, and electrocatalytic hydrogenation. Unfortunately, its slow kinetics limits the commercialization of such applications. It is therefore highly imperative to develop highly robust electrocatalysts with high activity, long-term durability, and low noble-metal contents. Previously intensive efforts have been made to introduce the advancements on developing non-precious transition metal electrocatalysts and their OER mechanisms. Electronic structure tuning is one of the most effective and interesting ways to boost OER activity and spin angular momentum is an intrinsic property of the electron. Therefore, modulation on the spin states and the magnetic properties of the electrocatalyst enables the changes on energy associated with interacting electron clouds with radical absorbance, affecting the OER activity and stability. Given that few review efforts have been made on this topic, in this review, the-state-of-the-art research progress on spin-dependent effects in OER will be briefed. Spin engineering strategies, such as strain, crystal surface engineering, crystal doping, etc., will be introduced. The related mechanism for spin manipulation to boost OER activity will also be discussed. Finally, the challenges and prospects for the development of spin catalysis are presented. This review aims to highlight the significance of spin engineering in breaking the bottleneck of electrocatalysis and promoting the practical application of high-efficiency electrocatalysts.

Ce Single-Atom Incorporation Enhances the Oxygen Evolution Reaction of Co3O4 in Acid.

Oxygen evolution reaction (OER) plays an important role in energy conversion processes such as water electrolysis and metal-air batteries. At present, finding a high-performance and low-cost catalyst for the OER in acidic media remains a great challenge. It is therefore important to develop efficient, robust, and inexpensive electrocatalysts by replacing noble metal-based catalysts with transition-metal electrocatalysts. Herein, we propose a facile method for incorporating Ce-metal single atoms into Co3O4 nanosheets to boost their OER activity and stability. Owing to the enhanced charge transfer and improved electronic structure resulting from Ce incorporation, the obtained Ce single-atom-doped Co3O4 nanosheet exhibits greatly enhanced OER performance. It achieves a 10 mA cm-2 current density under a low overpotential of 348 mV in a 0.5 M H2SO4 solution with excellent stability, outperforming the state-of-the-art non-noble electrocatalysts recently reported in acid.

Transmission dynamics and phylogeography of Mycobacterium tuberculosis in China based on whole-genome phylogenetic analysis.

OBJECTIVES: This study aimed to describe the lineage-specific transmissibility and epidemiological migration of Mycobacterium tuberculosis in China. METHODS: We curated a large set of whole-genome sequences from 3204 M. tuberculosis isolates, including thousands of newly sequenced genomes, and applied a series of metrics to compare the transmissibility of M. tuberculosis strains between lineages and sublineages. The countrywide transmission patterns of major lineages were explored. RESULTS: We found that lineage 2 (L2) was the most prevalent lineage in China (85.7%), with the major sublineage 2.2.1 (80.9%), followed by lineage 4 (L4) (13.8%), which comprises major sublineages 4.2 (1.5%), 4.4 (6.2%) and 4.5 (5.8%). We showed evidence for frequent cross-regional spread and large cluster formation of L2.2.1 strains, whereas L4 strains were relatively geographically restricted in China. Next, we applied a series of genomic indices to evaluate M. tuberculosis strain transmissibility and uncovered higher transmissibility of L2.2.1 compared with the L2.2.2 and L4 sublineages. Phylogeographic analysis showed that southern, eastern, and northern China were highly connected regions for countrywide L2.2.1 strain spread. CONCLUSIONS: The present study provides insights into the different transmission and migration patterns of the major M. tuberculosis lineages in China and highlights that transmissible L2.2.1 is a threat to tuberculosis control.

Modulated Electronic Structure of Co3O4 by Single Atoms for Efficient Anodic Oxygen Evolution in Acid.

The challenge of the practical application of a water electrolyzer system lies in the development of low-manufacturing cost, highly active, and stable electrocatalysts to replace the noble metal ones, in order to enable environmentally friendly hydrogen production on a large scale. Herein, a facile method is proposed for boosting the performance of Co3O4 through the incorporation of large-sized single atoms. Due to the larger ionic radius of rare earth metals than that of Co, the incorporation elongates the bond length of Co─O, resulting in the narrowed d-p band centers and the high spin configuration, which is favorable for the interaction and charge transfer with absorbent (*OH). As a result, the Ce-incorporated Co3O4 with the longest Co─O bond length exhibits the best oxygen evolution reaction (OER) performance, specifically, the turnover frequency is over 17 times higher than that of pristine Co3O4 nanosheet under an overpotential of 400 mV. Powered by a commercial Si solar cell, a two-electrode solar water-splitting device combining Ce-incorporated Co3O4 and Pt delivers a solar-to-hydrogen conversion efficiency of 13.53%. The strategy could provide a new insight for improving the performance of OER electrocatalysts in acid toward practical applications.

Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China.

OBJECTIVES: We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. METHODS: We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. RESULT: The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. CONCLUSION: MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.

Electron-Withdrawing Substituents Allow Boosted NIR-II Fluorescence in J-Type Aggregates for Bioimaging and Information Encryption.

Developing molecular fluorophores with enhanced fluorescence in aggregate state for the second near-infrared (NIR-II) imaging is highly desirable but remains a tremendous challenge due to the lack of reliable design guidelines. Herein, we report an aromatic substituent strategy to construct highly bright NIR-II J-aggregates. Introduction of electron-withdrawing substituents at 3,5-aryl and meso positions of classic boron dipyrromethene (BODIPY) skeleton can promote slip-stacked J-type arrangement and further boost NIR-II fluorescence of J-aggregates via increased electrostatic repulsion and intermolecular hydrogen bond interaction. Notably, NOBDP-NO2 with three nitro groups (-NO2 ) shows intense NIR-II fluorescence at 1065 nm and high absolute quantum yield of 3.21 % in solid state, which can be successfully applied in bioimaging, high-level encoding encryption, and information storage. Moreover, guided by this electron-withdrawing substituent strategy, other skeletons (thieno-fused BODIPY, aza-BODIPY, and heptamethine cyanine) modified with -NO2 are converted into J-type aggregates with enhanced NIR-II fluorescence, showing great potential to convert aggregation caused emission quenching (ACQ) dyes into brilliant J-aggregates. This study provides a universal method for construction of strong NIR-II emissive J-aggregates by rationally manipulating molecular packing and establishing relationships among molecular structures, intermolecular interactions, and fluorescence properties.

Modular Design of Biodegradable Ionizable Lipids for Improved mRNA Delivery and Precise Cancer Metastasis Delineation In Vivo.

Lipid nanoparticles (LNPs) represent the most clinically advanced nonviral mRNA delivery vehicles; however, the full potential of the LNP platform is greatly hampered by inadequate endosomal escape capability. Herein, we rationally introduce a disulfide bond-bridged ester linker to modularly synthesize a library of 96 linker-degradable ionizable lipids (LDILs) for improved mRNA delivery in vivo. The top-performing LDILs are composed of one 4A3 amino headgroup, four disulfide bond-bridged linkers, and four 10-carbon tail chains, whose unique GSH-responsive cone-shaped architectures endow optimized 4A3-SCC-10 and 4A3-SCC-PH lipids with superior endosomal escape and rapid mRNA release abilities, outperforming their parent lipids 4A3-SC-10/PH without a disulfide bond and control lipids 4A3-SSC-10/PH with a disulfide bond in the tail. Notably, compared to DLin-MC3-DMA via systematic administration, 4A3-SCC-10- and 4A3-SCC-PH-formulated LNPs significantly improved mRNA delivery in livers by 87-fold and 176-fold, respectively. Moreover, 4A3-SCC-PH LNPs enabled the highly efficient gene editing of 99% hepatocytes at a low Cre mRNA dose in tdTomato mice following intravenous administration. Meanwhile, 4A3-SCC-PH LNPs were able to selectively deliver firefly luciferase mRNA and facilitate luciferase expression in tumor cells after intraperitoneal injection, further improving cancer metastasis delineation and surgery via bioluminescence imaging. We envision that the chemistry adopted here can be further extended to develop new biodegradable ionizable lipids for broad applications such as gene editing and cancer immunotherapy.

Comparison of Short-Tau Inversion Recovery With Short-Tau Inversion Recovery-Slice Encoding for Metal Artifact Correction for Spine Imaging at 1.5 T in the Setting of Metallic Implants.

OBJECTIVE: To compare the image quality of short-tau inversion recovery (STIR) and the STIR-slice encoding for metal artifact correction (SEMAC) sequence for postsurgery spine magnetic resonance imaging (MRI). METHODS: Twenty-nine patients with metallic spinal implants who underwent spinal 1.5 T MRI with STIR and STIR-SEMAC sequences between July 2016 and November 2020 were retrospectively enrolled. Qualitative assessments were performed using 5-point scales; higher scores indicated better image quality. For screw metal artifact analysis, scores were obtained for artifacts on vertebral bodies and neural foramina, screw artifact widths, and bone marrow signal intensities. For patient-based analysis, scores were obtained for imaging quality and fat suppression quality, signal intensity, and cerebrospinal fluid noise. A paired t test was performed for statistical analyses. RESULTS: We analyzed 163 screws in 29 patients. In the screw metal artifact analysis, the vertebral body and neural foramen scores were significantly higher for the STIR-SEMAC images than for the STIR (all P < 0.001). The artifact width in the STIR-SEMAC images (9.8 ± 3.4 mm) was significantly smaller than that in the STIR images (16.0 ± 4.7 mm, P < 0.001). In patient-based analysis, the fat suppression and imaging quality scores were significantly higher for the STIR-SEMAC images than for the STIR images (all P < 0.001). The cerebrospinal fluid signal intensity, noise, and signal-to-noise ratios were significantly higher for the STIR images (all P < 0.005). CONCLUSIONS: Short-tau inversion recovery-SEMAC sequences provide good metallic artifact reduction and fat suppression for postsurgery spine 1.5 T MRI.

Non-Solvatochromic Cell Membrane-Targeted NIR Fluorescent Probe for Visualization of Polarity Abnormality in Drug-Induced Liver Injury Mice.

Noninvasive visualization of liver polarity by using fluorescence imaging technology is helpful to better understand drug-induced liver injury (DILI). However, cell membrane-targeted polarity-sensitive near-infrared (NIR) fluorescent probes are still scarce. Herein, we report a non-solvatochromic cell membrane-targeted NIR small molecular probe (N-BPM-C10) for monitoring the polarity changes on cell membranes in living cells and in vivo. N-BPM-C10 exhibits polarity-dependent fluorescence around 655 nm without an obvious solvatochromic effect, which endows it with good capability for the in vivo imaging study. Moreover, it can rapidly and selectively light up the cell membranes as well as distinguish tumor cells from normal cells due to its excellent polarity-sensitive ability. More importantly, N-BPM-C10 has been successfully applied to visualize liver polarity changes in vivo, revealing the reduction of liver polarity in DILI mice. We believe that N-BPM-C10 provides a new way for the diagnosis of DILI.

A pharmacokinetic-pharmacodynamic model based on the SSA-1DCNN-Attention network and the semicompartment method.

To solve the problem of inaccurate prediction caused by the lack of representativeness of samples due to the small sample size of the collected clinical data when using machine learning methods to predict drug concentration in plasma and describe the hysteresis phenomenon of drug effect lagging behind plasma drug concentration, this paper proposes a pharmacokinetic-pharmacodynamic (PK-PD) model based on the SSA-1DCNN-Attention network and the semicompartment method. First, a one-dimensional convolutional neural network (1DCNN) is established, and the attention mechanism is introduced to determine the importance of each physiological and biochemical parameter. The sparrow search algorithm (SSA) is used to optimize the parameters of the network to improve the prediction accuracy after data enhancement through the synthetic minority oversampling technique (SMOTE) method. After constructing the time-concentration relationship of the drug through the SSA-1DCNN-Attention network, the concentration-effect relationship of the drug is established by using the semicompartment method to synchronize the drug effect with the concentration. At last, the phenobarbital (PHB) combined with Cynanchum otophyllum saponins to treat epilepsy was taken as an example to validate the proposed method.

A pharmacokinetic model based on the SSA-1DCNN-Attention method.

To solve the problem of the lack of representativeness of the training set and the poor prediction accuracy due to the limited number of training samples when the machine learning method is used for the classification and prediction of pharmacokinetic indicators, this paper proposes a 1DCNN-Attention concentration prediction model optimized by the sparrow search algorithm (SSA). First, the SMOTE method is used to expand the small sample experimental data to make the data diverse and representative. Then a one-dimensional convolutional neural network (1DCNN) model is established, and the attention mechanism is introduced to calculate the weight of each variable for dividing the importance of each pharmacokinetic indicator by the output drug concentration. The SSA algorithm was used to optimize the parameters in the model to improve the prediction accuracy after data expansion. Taking the pharmacokinetic model of phenobarbital (PHB) combined with Cynanchum otophyllum saponins to treat epilepsy as an example, the concentration changes of PHB were predicted and the effectiveness of the method was verified. The results show that the proposed model has a better prediction effect than other methods.

Structural and DNA end resection study of the bacterial NurA-HerA complex.

BACKGROUND: The nuclease NurA and the ATPase/translocase HerA play a vital role in repair of double-strand breaks (DSB) during the homologous recombination in archaea. A NurA-HerA complex is known to mediate DSB DNA end resection, leading to formation of a free 3' end used to search for the homologous sequence. Despite the structures of individual archaeal types of NurA and HerA having been reported, there is limited information regarding the molecular mechanisms underlying this process. Some bacteria also possess homologs of NurA and HerA; however, the bacterial type of this complex, as well as the detailed mechanisms underlying the joining of NurA-HerA in DSB DNA end resection, remains unclear. RESULTS: We report for the first time the crystal structures of Deinococcus radiodurans HerA (drHerA) in the nucleotide-free and ADP-binding modes. A D. radiodurans NurA-HerA complex structure was constructed according to a low-resolution cryo-electron microscopy map. We performed site-directed mutagenesis to map the drNurA-HerA interaction sites, suggesting that their interaction is mainly mediated by ionic links, in contrast to previously characterized archaeal NurA-HerA interactions. The key residues responsible for the DNA translocation activity, DNA unwinding activity, and catalytic activities of the drNurA-HerA complex were identified. A HerA/FtsK-specific translocation-related motif (TR motif) that guarantees the processivity of double-stranded DNA (dsDNA) translocation was identified. Moreover, a mechanism for the translocation-regulated resection of the 5' tail of broken dsDNA and the corresponding generation of a recombinogenic 3' single-stranded DNA tail by the drNurA-HerA complex was elucidated. CONCLUSIONS: Our work provides new insights into the mechanism underlying bacterial NurA-HerA-mediated DSB DNA end resection, and the way this complex digests the 5' tail of a DNA duplex and provides long 3' free end for strand invasion in the bacterial homologous recombination process.

Macrophage migration inhibitory factor MtMIF3 prevents the premature aging of Medicago truncatula nodules.

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine involved in immune response in animals. However, the role of MIFs in plants such as Medicago truncatula, particularly in symbiotic nitrogen fixation, remains unclear. An investigation of M. truncatula-Sinorhizobium meliloti symbiosis revealed that MtMIF3 was mainly expressed in the nitrogen-fixing zone of the nodules. Silencing MtMIF3 using RNA interference (Ri) technology resulted in increased nodule numbers but higher levels of bacteroid degradation in the infected cells of the nitrogen-fixing zone, suggesting that premature aging was induced in MtMIF3-Ri nodules. In agreement with this conclusion, the activities of nitrogenase, superoxide dismutase and catalase were lower than those in controls, but cysteine proteinase activity was increased in nodulated roots at 28 days postinoculation. In contrast, the overexpression of MtMIF3 inhibited nodule senescence. MtMIF3 is localized in the plasma membrane, nucleus, and cytoplasm, where it interacts with methionine sulfoxide reductase B (MsrB), which is also localized in the chloroplasts of tobacco leaf cells. Taken together, these results suggest that MtMIF3 prevents premature nodule aging and protects against oxidation by interacting with MtMsrB.

Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans.

Deinococcus radiodurans possesses robust DNA damage response and repair abilities, and this is mainly due to its efficient homologous recombination repair system, which incorporates an uncharacterized Holliday junction (HJ) resolution process. D. radiodurans encodes two putative HJ resolvase (HJR) homologs: RuvC (DrRuvC) and YqgF (DrYqgF). Here, both DrRuvC and DrYqgF were identified as essential proteins for the survival of D. radiodurans. The crystal structures and the biochemical properties of DrRuvC and DrYqgF were also studied. DrRuvC crystallized as a homodimer, while DrYqgF crystallized as a monomer. DrRuvC could preferentially cleave HJ at the consensus 5'-(G/C)TC↓(G/C)-3' sequence and could prefer using Mn2+ for catalysis in vitro, which would be different from the preferences of the other previously characterized RuvCs. On the other hand, DrYqgF was identified as a Mn2+-dependent RNA 5'-3' exo/endonuclease with a sequence preference for poly(A) and without any HJR activity. IMPORTANCE Deinococcus radiodurans is one of the most radioresistant bacteria in the world due to its robust DNA damage response and repair abilities, which are contributed by its efficient homologous recombination repair system. However, the late steps of homologous recombination, especially the Holliday junction (HJ) resolution process, have not yet been well-studied in D. radiodurans. We characterized the structural and biochemical features of the two putative HJ resolvases, DrRuvC and DrYqgF, in D. radiodurans. It was identified that DrRuvC and DrYqgF exhibit HJ resolvase (HJR) activity and RNA exo/endonuclease activity, respectively. Furthermore, both DrRuvC and DrYqgF digest substrates in a sequence-specific manner with a preferred sequence that is different from those of the other characterized RuvCs or YqgFs. Our findings provide new insights into the HJ resolution process and reveal a novel RNase involved in RNA metabolism in D. radiodurans.

A deep learning-based method for the diagnosis of vertebral fractures on spine MRI: retrospective training and validation of ResNet.

PURPOSE: To improve the performance of less experienced clinicians in the diagnosis of benign and malignant spinal fracture on MRI, we applied the ResNet50 algorithm to develop a decision support system. METHODS: A total of 190 patients, 50 with malignant and 140 with benign fractures, were studied. The visual diagnosis was made by one senior MSK radiologist, one fourth-year resident, and one first-year resident. The MSK radiologist also gave the binary score for 15 qualitative imaging features. Deep learning was implemented using ResNet50, using one abnormal spinal segment selected from each patient as input. The T1W and T2W images of the lesion slice and its two neighboring slices were considered. The diagnostic performance was evaluated using tenfold cross-validation. RESULTS: The overall reading accuracy was 98, 96, and 66% for the senior MSK radiologist, fourth-year resident, and first-year resident, respectively. Of the 15 imaging features, 10 showed a significant difference between benign and malignant groups with p < = 0.001. The accuracy achieved by using the ResNet50 deep learning model for the identified abnormal vertebral segment was 92%. Compared to the first-year resident's reading, the model improved the sensitivity from 78 to 94% (p < 0.001) and the specificity from 61 to 91% (p < 0.001). CONCLUSION: Our deep learning-based model may provide information to assist less experienced clinicians in the diagnosis of spinal fractures on MRI. Other findings away from the vertebral body need to be considered to improve the model, and further investigation is required to generalize our findings to real-world settings.

Novel application of Ag/PbBiO2I nanocomposite in piezocatalytic degradation of rhodamine B via harvesting ultrasonic vibration energy.

Ag/PbBiO2I nanocomposite was synthesized and firstly applied in piezocatalytic degradation of rhodamine B (RhB) under ultrasonic vibration. The two-dimensional structure endows PbBiO2I nanosheets piezoelectric property, so that it can drive the piezocatalytic reaction under ultrasonic vibration. The loading of Ag nanoparticles forms Schottky barriers between the Ag-PbBiO2I contact region, which improves the separation of charge carriers and subsequently increases the piezocatalytic efficiency. The RhB degradation rate of the optimal Ag/PbBiO2I sample is 0.0165 min-1, which reaches 6.8 times that of pure PbBiO2I. This work indicates that the PbBiO2I nanosheet shows promising potential in utilizing ultrasonic vibration energy.