Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from Bacillus thuringiensis.

A riboswitch generally regulates the expression of its downstream genes through conformational change in its expression platform (EP) upon ligand binding. The cyclic diguanosine monophosphate (c-di-GMP) class I riboswitch Bc1 is widespread and conserved among Bacillus cereus group species. In this study, we revealed that Bc1 has a long EP with two typical ρ-independent terminator sequences 28 bp apart. The upstream terminator T1 is dominant in vitro, while downstream terminator T2 is more efficient in vivo. Through mutation analysis, we elucidated that Bc1 exerts a rare and incoherent "transcription-translation" dual regulation with T2 playing a crucial role. However, we found that Bc1 did not respond to c-di-GMP under in vitro transcription conditions, and the expressions of downstream genes did not change with fluctuation in intracellular c-di-GMP concentration. To explore this puzzle, we conducted SHAPE-MaP and confirmed the interaction of Bc1 with c-di-GMP. This shows that as c-di-GMP concentration increases, T1 unfolds but T2 remains almost intact and functional. The presence of T2 masks the effect of T1 unwinding, resulting in no response of Bc1 to c-di-GMP. The high Shannon entropy values of EP region imply the potential alternative structures of Bc1. We also found that zinc uptake regulator can specifically bind to the dual terminator coding sequence and slightly trigger the response of Bc1 to c-di-GMP. This work will shed light on the dual-regulation riboswitch and enrich our understanding of the RNA world.IMPORTANCEIn nature, riboswitches are involved in a variety of metabolic regulation, most of which preferentially regulate transcription termination or translation initiation of downstream genes in specific ways. Alternatively, the same or different riboswitches can exist in tandem to enhance regulatory effects or respond to multiple ligands. However, many putative conserved riboswitches have not yet been experimentally validated. Here, we found that the c-di-GMP riboswitch Bc1 with a long EP could form a dual terminator and exhibit non-canonical and incoherent "transcription-translation" dual regulation. Besides, zinc uptake regulator specifically bound to the coding sequence of the Bc1 EP and slightly mediated the action of Bc1. The application of SHAPE-MaP to the dual regulation mechanism of Bc1 may establish the foundation for future studies of such complex untranslated regions in other bacterial genomes.

Association between the fetal-type posterior cerebral artery and intracranial anterior and posterior circulating atherosclerotic plaques using multi-contrast magnetic resonance vessel wall imaging.

Background: Intracranial atherosclerotic disease (ICAD) is one of the most common causes of ischemic stroke. The fetal-type posterior cerebral artery (FTP) affects intracranial collateral circulation, which is closely related to the occurrence and development of ICAD. Knowledge of the relationship between FTP and ICAD is important for developing treatment strategies for FTP patients diagnosed with atherosclerotic diseases. This study aims to quantitatively analyze the association between the FTP and intracranial atherosclerotic plaques using magnetic resonance vessel wall imaging (VW-MRI). Methods: This retrospective study enrolled patients with recent cerebrovascular symptoms (stroke or transient ischemic attack <2 weeks) who were diagnosed with atherosclerotic plaque(s) by VW-MRI in one hospital from October 2018 to March 2022. They were classified into the FTP group and the non-FTP group. Plaque characteristics and vascular-related parameters in intracranial arteries were compared between the two groups. Univariate and multivariate logistic regressions were performed to determine the odds ratios (ORs) and corresponding 95% confidence intervals (CIs) of the plaque characteristics between the two groups. Results: A total of 104 patients (mean age: 61.8±9.8 years, 57 males) were included for VW-MRI scan analysis. 40 (38.46%) and 64 (61.54%) were classified into the FTP and the non-FTP groups, respectively. The plaques of middle cerebral artery (MCA) in the FTP group were more likely to occur on the dorsal and superior walls of the lumen compared with the non-FTP group (37.50% vs. 17.19%, P=0.001). The remodeling index (RI) of MCA was statistically different between the two groups (1.071±0.267 vs. 0.886±0.235, P=0.007). No significant differences were found in vertebrobasilar artery (VBA) plaque distributions (17.50% vs. 9.38%, 10.00% vs. 12.50%, 20.00% vs. 17.19%, P>0.05) and characteristics between the two groups (RI: 1.095±0.355 vs. 0.978±0.251; eccentricity index: 0.539±1.622 vs. 0.550±0.171, P>0.05). Conclusions: The plaques in the FTP group were more likely to occur on the dorsal and superior walls of the MCA, and the presentence of FTP was found to be significantly correlated with vascular remodeling of MCA atherosclerotic plaques. The relationship between the severity of intracranial atherosclerosis and the presence of FTP can provide valuable information for clinicians to intervene early and prevent the occurrence of stroke.

Multiparameter prediction model of immune checkpoint inhibitors combined with chemotherapy for non-small cell lung cancer based on support vector machine learning.

The reliable predictive markers to identify which patients with advanced non-small cell lung cancer tumors (NSCLC) will achieve durable clinical benefit (DCB) for chemo-immunotherapy are needed. In this retrospective study, we collected radiomics and clinical signatures from 94 patients with advanced NSCLC treated with anti-PD-1/PD-L1 combined with chemotherapy from January 1, 2018 to May 31, 2022. Radiomics variables were extracted from pretreatment CT and selected by Spearman correlation coefficients and clinical features by Logistics regression analysis. We performed effective diagnostic algorithms principal components analysis (PCA) and support vector machine (SVM) to develop an early classification model among DCB and non-durable benefit (NDB) groups. A total of 26 radiomics features and 6 clinical features were selected, and then principal component analysis was used to obtain 6 principal components for SVM building. RC-SVM achieved prediction accuracy with AUC of 0.91 (95% CI 0.87-0.94) in the training set, 0.73 (95% CI 0.61-0.85) in the cross-validation set, 0.84 (95% CI 0.80-0.89) in the external validation set. The new method of RC-SVM model based on radiomics-clinical signatures provides a significant additive value on response prediction in patients with NSCLC preceding chemo-immunotherapy.

Cytobacillus citreus sp. nov., isolated from citrus rhizosphere soil.

A Gram-stain-positive, rod-shaped and motile strain, designated FJAT-49705T, was isolated from the citrus rhizosphere soil sample. Strain FJAT-49705T grew at 20-40 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, pH 7.0) with 0-5 % (w/v) NaCl (optimum, 2 %). Strain FJAT-49705T showed high 16S rRNA gene sequence similarity to 'Bacillus dafuensis' FJAT-25496T (99.7 %) and Cytobacillus solani FJAT-18043T (98.0 %). In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees (based on 71 bacterial single-copy genes), strain FJAT-49705T clustered with the members of the genus Cytobacillus. MK-7 was the only isoprenoid quinone present. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 36.9 %. The average nucleotide identity (ANI) values between FJAT-49705T and 'B. dafuensis' FJAT-25496T and C. solani FJAT-18043T were below the cut-off level (95-96 %) recommended as the ANI criterion for interspecies identity. Based on the above results, strain FJAT-49705T represents a novel species of the genus Cytobacillus, for which the name Cytobacillus citreus sp. nov. is proposed. The type strain is FJAT-49705T (=CCTCC AB 2019243T= LMG 31580T).

Temperature drives the assembly of Bacillus community in mangrove ecosystem.

Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO3-N and NH4-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.

Genome-based reclassification of Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer of Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb. nov. and Evansella tamaricis comb. nov.

In the present study, the taxonomic positions of Evansella polygoni, Evansella clarkii, Bacillus shivajii and Bacillus tamaricis were evaluated using phylogenetic and genome-based comparisons. In phylogenetic (based on 16S rRNA sequencing) and phylogenomic (based on concatenation of protein-marker genes) trees, Bacillus shivajii and Bacillus tamaricis were placed between genera Evansella and Alteribacter. The amino acid identity (AAI) values suggested that Bacillus shivajii and Bacillus tamaricis were members of the genus Evansella. The average nucleotide identity (ANI) value between Evansella polygoni and Evansella clarkii was higher than the threshold values for bacterial species delineation, indicating that they belong to the same species. Based on the results, we propose to reclassify Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb. nov. and Evansella tamaricis comb. nov.

Manganese-promoted cleavage of acetylacetonate resembling the ß-diketone cleaving dioxygenase (Dke1) reactivity.

We here report a manganese-based oxidative cleavage of inactivated acetylacetonate, the mechanistic pathway of which resembles Dke1-catalyzed reactions of ß-diketone and α-keto acid. This oxidative transformation proceeds through an acetylacetonate-pyruvate-oxalate pathway, which can be terminated at the stage of pyruvate through ligand/solvent variation. XRD, time-dependent GC-MS, and isotope-labeling studies suggested that our system represents the same cleaving specificity and dioxygenase-like reactivity of Dke1.

Pentanuclear clusters resembling the cubane-dangler connectivity in the native oxygen-evolving center of photosystem II.

A series of pentametallic "cubane-plus-dangler" complexes have been target synthesized. Among them, the [Fe3Ni2] aggregate strongly resembled the native oxygen-evolving center by mimicking the "cubane-plus-dangler" skeleton, the aqua binding site, and the connectivity between the pendent ion and the parent cubane. Our synthetic strategy that uses tri-substituted methanol as the "cubane-generator" and carboxylate as the pendant ligand provides a feasible approach for accessing model compounds of biological catalyst systems.