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.

An Improved Self-Adaptive Differential Evolution with the Neighborhood Search Algorithm for Global Optimization of Bimetallic Clusters.

Global optimization of multicomponent cluster structures is considerably time-consuming due to the existence of a vast number of isomers. In this work, we proposed an improved self-adaptive differential evolution with the neighborhood search (SaNSDE) algorithm and applied it to the global optimization of bimetallic cluster structures. The cross operation was optimized, and an improved basin hopping module was introduced to enhance the searching efficiency of SaNSDE optimization. Taking (PtNi)N (N = 38 or 55) bimetallic clusters as examples, their structures were predicted by using this algorithm. The traditional SaNSDE algorithm was carried out for comparison with the improved SaNSDE algorithm. For all the optimized clusters, the excess energy and the second difference of the energy were calculated to examine their relative stabilities. Meanwhile, the bond order parameters were adopted to quantitatively characterize the cluster structures. The results reveal that the improved SaNSDE algorithm possessed significantly higher searching capability and faster convergence speed than the traditional SaNSDE algorithm. Furthermore, the lowest-energy configurations of (PtNi)38 clusters could be classified as the truncated octahedral and disordered structures. In contrast, all the optimal (PtNi)55 clusters were approximately icosahedral. Our work fully demonstrates the high efficiency of the improved algorithm and advances the development of global optimization algorithms and the structural prediction of multicomponent clusters.

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.

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.

Polyketide synthases mutation in tuberculosis transmission revealed by whole genomic sequence, China, 2011-2019.

Introduction: Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis (Mtb). Previous studies have primarily focused on the transmissibility of multidrug-resistant (MDR) or extensively drug-resistant (XDR) Mtb. However, variations in virulence across Mtb lineages may also account for differences in transmissibility. In Mtb, polyketide synthase (PKS) genes encode large multifunctional proteins which have been shown to be major mycobacterial virulence factors. Therefore, this study aimed to identify the role of PKS mutations in TB transmission and assess its risk and characteristics. Methods: Whole genome sequences (WGSs) data from 3,204 Mtb isolates was collected from 2011 to 2019 in China. Whole genome single nucleotide polymorphism (SNP) profiles were used for phylogenetic tree analysis. Putative transmission clusters (≤10 SNPs) were identified. To identify the role of PKS mutations in TB transmission, we compared SNPs in the PKS gene region between "clustered isolates" and "non-clustered isolates" in different lineages. Results: Cluster-associated mutations in ppsA, pks12, and pks13 were identified among different lineage isolates. They were statistically significant among clustered strains, indicating that they may enhance the transmissibility of Mtb. Conclusion: Overall, this study provides new insights into the function of PKS and its localization in M. tuberculosis. The study found that ppsA, pks12, and pks13 may contribute to disease progression and higher transmission of certain strains. We also discussed the prospective use of mutant ppsA, pks12, and pks13 genes as drug targets.

Thermally activated microstructural evolution of metallic heterophase nanoparticles: insights from molecular dynamics simulations.

A crystal phase is a key factor to determine the physical and chemical properties of crystalline materials. As a new class of nanoscale structures, heterophase nanoparticles, which assemble conventional and unconventional phases, exhibit exceptional properties in comparison with their single-phase counterparts. In this work, we explored the thermodynamic stability of Au, Co, and AuCo heterophase nanoparticles with fcc and hcp phases by using molecular dynamics simulations. These heterostructured nanoparticles were continuously heated to examine their thermally activated structural evolutions. Au and Co single-phase nanoparticles were also considered for comparison. The results show that the phase transition between fcc and hcp is absent in these heterophase nanoparticles despite the existence of an unconventional phase. Although the melting of Au and Co heterophase nanoparticles is homogeneous, AuCo heterophase nanoparticles show heterogeneous melting, i.e., the Au fcc domain firstly melts, followed by the melting of the Co hcp domain, exhibiting a typical two-stage melting characteristic and resulting in the existence of a solid-core/liquid-shell structure within a considerable temperature region. Furthermore, the mutual diffusion of atoms between fcc and hcp domains is observed in the Au and Co heterophase nanoparticles. However, the unidirectional diffusion from the Au domain to the Co domain is found in the AuCo heterophase nanoparticles prior to their overall melting. This study deepens the fundamental understanding of the thermodynamic evolution of metallic heterogeneous nanoparticles and provides mechanistic and quantitative guidance for the rational design and applications of nanoscale multiphase heterostructures.

Structural Evolution of the Surface and Interface in Bimetallic High-Index Faceted Heterogeneous Nanoparticles.

Bimetallic high-index faceted heterostructured nanoparticles represent a new class of high-performance nanocatalysts. In this work, we investigated the structural evolution of PtAu tetrahexahedral heterostructured nanoparticles enclosed by {210} facets using molecular dynamics simulations. The surface and interface were specifically addressed. The results show that the PtAu nanoparticle exhibits a heterogeneous melting pattern, leading to solid-liquid coexistence over a wide temperature range. In terms of particle shape evolution, the critical transformation temperature for the surface structure of the PtAu heterostructured nanoparticle is much lower than the melting point of each domain. In comparison, the interface could be basically retained even when the Au domain completely melts. These results extend our fundamental understanding of the thermally driven structural evolution of the surface and interface in bimetallic high-index faceted heterostructured nanoparticles and provide insight into the design and application of metallic nanoparticles with multifunctional performance.

Long Non-Coding RNA THOR Depletion Inhibits Human Non-Small Cell Lung Cancer Cell Growth.

Long non-coding RNA (LncRNA) THOR (Lnc-THOR) is expressed in testis and multiple human malignancies. Lnc-THOR association with IGF2BP1 (IGF2 mRNA-binding protein 1) is essential for stabilization and transcription of IGF2BP1 targeted mRNAs. We tested its expression and potential functions in non-small cell lung cancer (NSCLC). In primary NSCLC cells and established cell lines, Lnc-THOR shRNA or CRISPR/Cas9-mediated knockout (KO) downregulated IGF2BP1 target mRNAs (IGF2, Gli1, Myc and SOX9), inhibiting cell viability, growth, proliferation, migration and invasion. Significant apoptosis activation was detected in Lnc-THOR-silenced/-KO NSCLC cells. Conversely, ectopic overexpression of Lnc-THOR upregulated IGF2BP1 mRNA targets and enhanced NSCLC cell proliferation, migration and invasion. RNA-immunoprecipitation and RNA pull-down assay results confirmed the direct binding between Lnc-THOR and IGF2BP1 protein in NSCLC cells. Lnc-THOR silencing and overexpression were ineffective in IGF2BP1-KO NSCLC cells. Forced IGF2BP1 overexpression failed to rescue Lnc-THOR-KO NSCLC cells. In vivo, intratumoral injection of Lnc-THOR shRNA adeno-associated virus potently inhibited A549 xenograft tumor growth in nude mice. At last we show that Lnc-THOR is overexpressed in multiple NSCLC tissues and established/primary NSCLC cells. Collectively, these results highlighted the ability of Lnc-THOR in promoting NSCLC cell growth by associating with IGF2BP1, suggesting that Lnc-THOR represents a promising therapeutic target of NSCLC.

Safety and effectiveness of a Tai Chi-based cardiac rehabilitation programme for chronic coronary syndrom patients: study protocol for a randomised controlled trial.

INTRODUCTION: Preliminary evidence from clinical observations suggests that Tai Chi exercise may offer potential benefits for patients with chronic coronary syndrom (CCS). However, the advantages for CCS patients to practice Tai Chi exercise as rehabilitation have not been rigorously tested and there is a lack of consensus on its benefits. This study aims to develop an innovative Tai Chi Cardiac Rehabilitation Program (TCCRP) for CCS patients and to assess the efficacy, safety and acceptability of the programme. METHODS AND ANALYSIS: We propose to conduct a multicentre randomised controlled clinical trial comprising of 150 participants with CCS. The patients will be randomly assigned in a 1:1 ratio into two groups. The intervention group will participate in a supervised TCCRP held three times a week for 3 months. The control group will receive supervised conventional exercise rehabilitation held three times a week for 3 months. The primary and secondary outcomes will be assessed at baseline, 1 month, 3 months after intervention and after an additional 3-month follow-up period. Primary outcome measures will include a score of 36-Item Short Form Survey and Chinese Perceived Stress Scale. The secondary outcome measures will include body composition, cardiopulmonary exercise test, respiratory muscle function, locomotor skills, echocardiogram, New York Heart Association classification, heart rate recovery time and laboratory examination. Other measures also include Seattle Angina Scale, Pittsburgh Sleep Quality Index, Patient Health Questionnaire-9, Generalized Anxiety Disorder-7 and Berg Balance Scale. All adverse events will be recorded and analysed. ETHICS AND DISSEMINATION: This study conforms to the principles of the Declaration of Helsinki and relevant ethical guidelines. Ethical approval has been obtained from the Ethics Committee of Chinese People's Libration Army General Hospital (approval number: S2019-060-02). Findings from this study will be published and presented at conferences for widespread dissemination of the results. TRIAL REGISTRATION NUMBER: NCT03936504.

Expression of eosinophils be beneficial to early clinical diagnosis of brucellosis.

OBJECTIVE: Investigate the expression and significance of eosinophils in brucellosis. METHODS: Retrospective analysis of clinical data for 151 brucellosis patients (BR group), complete blood count and blood bacterial culture etc.; in addition, 150 general bacterial infection patients (BI group) and 135 persons in healthy physical condition upon testing (NC group) are selected respectively as the control groups to comparatively study expression of white blood cells and eosinophils for brucellosis patients. Adopt t test to compare measurement data. RESULTS: In comparison with BI group, WBC, NE, EO, MO, NE% and EO% in BR group are reduced but LY, LY% and MO% are increased and such difference shows statistical significance (P<0.01). In comparison with NC group, difference of WBC and NE in BR group shows no statistical significance (P>0.05). NE%, EO and EO% are reduced but MO, LY% and MO% are increased and such difference shows statistical significance (P<0.01). LY is increased and the difference shows statistical significance (P<0.05). White blood cell count is normal or is reduced among most of Brucellosis patients, accounting for 90.73% (137/151); the patients whose eosinophils are reduced account for 75.50% (114/151) and those whose eosinophils disappear are about 18.54% (28/151). CONCLUSION: There is an incidence rate of eosinophils decrease or disappearance in Brucellosis and it shows the indication significance in the diagnosis of early disease.

Utility of surface pollen assemblages to delimit Eastern Eurasian steppe types.

Modern pollen records have been used to successfully distinguish between specific prairie types in North America. Whether the pollen records can be used to detect the occurrence of Eurasian steppe, or even to further delimit various steppe types was until now unclear. Here we characterized modern pollen assemblages of meadow steppe, typical steppe and desert steppe from eastern Eurasia along an ecological humidity gradient. The multivariate ordination of the pollen data indicated that Eurasian steppe types could be clearly differentiated. The different steppe types could be distinguished primarily by xerophilous elements in the pollen assemblages. Redundancy analysis indicated that the relative abundances of Ephedra, Tamarix, Nitraria and Zygophyllaceae were positively correlated with aridity. The relative abundances of Ephedra increased from meadow steppe to typical steppe and desert steppe. Tamarix and Zygophyllaceae were found in both typical steppe and desert steppe, but not in meadow steppe. Nitraria was only found in desert steppe. The relative abundances of xerophilous elements were greater in desert steppe than in typical steppe. These findings indicate that Eurasian steppe types can be differentiated based on recent pollen rain.