Genome-wide mapping of GlnR-binding sites reveals the global regulatory role of GlnR in controlling the metabolism of nitrogen and carbon in Paenibacillus polymyxa WLY78.

BACKGROUND: Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N2-fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) according to nitrogen availability, which is achieved by binding to the two GlnR-binding sites located in the nif promoter region. However, further study on the GlnR-mediated global regulation in this bacterium is still needed. RESULTS: In this study, global identification of the genes directly under GlnR control is determined by using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assays (EMSA). Our results reveal that GlnR directly regulates the transcription of 17 genes/operons, including a nif operon, 14 nitrogen metabolism genes/operons (glnRA, amtBglnK, glnA1, glnK1, glnQHMP, nasA, nasD1, nasD2EF, gcvH, ansZ, pucR, oppABC, appABCDF and dppABC) and 2 carbon metabolism genes (ldh3 and maeA1). Except for the glnRA and nif operon, the other 15 genes/operons are newly identified targets of GlnR. Furthermore, genome-wide transcription analyses reveal that GlnR not only directly regulates the expression of these 17 genes/operons, but also indirectly controls the expression of some other genes/operons involved in nitrogen fixation and the metabolisms of nitrogen and carbon. CONCLUSION: This study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.

Glutamine synthetase and GlnR regulate nitrogen metabolism in Paenibacillus polymyxa WLY78.

Paenibacillus polymyxa WLY78, a N2-fixing bacterium, has great potential use as a biofertilizer in agriculture. Recently, we have revealed that GlnR positively and negatively regulates the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) in P. polymyxa WLY78 by binding to two loci of the nif promoter according to nitrogen availability. However, the regulatory mechanisms of nitrogen metabolism mediated by GlnR in the Paenibacillus genus remain unclear. In this study, we have revealed that glutamine synthetase (GS) and GlnR in P. polymyxa WLY78 play a key role in the regulation of nitrogen metabolism. P. polymyxa GS (encoded by glnA within glnRA) and GS1 (encoded by glnA1) belong to distinct groups: GSI-α and GSI-ß. Both GS and GS1 have the enzyme activity to convert NH4+ and glutamate into glutamine, but only GS is involved in the repression by GlnR. GlnR represses transcription of glnRA under excess nitrogen, while it activates the expression of glnA1 under nitrogen limitation. GlnR simultaneously activates and represses the expression of amtBglnK and gcvH in response to nitrogen availability. Also, GlnR regulates the expression of nasA, nasD1D2, nasT, glnQHMP, and glnS. IMPORTANCE In this study, we have revealed that Paenibacillus polymyxa GlnR uses multiple mechanisms to regulate nitrogen metabolism. GlnR activates or represses or simultaneously activates and inhibits the transcription of nitrogen metabolism genes in response to nitrogen availability. The multiple regulation mechanisms employed by P. polymyxa GlnR are very different from Bacillus subtilis GlnR which represses nitrogen metabolism under excess nitrogen. Both GS encoded by glnA within the glnRA operon and GS1 encoded by glnA1 in P. polymyxa WLY78 are involved in ammonium assimilation, but only GS is required for regulating GlnR activity. The work not only provides significant insight into understanding the interplay of GlnR and GS in nitrogen metabolism but also provides guidance for improving nitrogen fixation efficiency by modulating nitrogen metabolism.

[Network Meta-analysis of Chinese medicine injections in treatment of rheumatoid arthritis].

This study aims to systematically evaluate the efficacy and safety of Chinese medicine injections in the treatment of rheumatoid arthritis. Specifically, randomized controlled trial(RCT) in the treatment of rheumatoid arthritis with Chinese medicine injections was retrieved from PubMed, EMbase, Cochrane Library, Web of Science, Wanfang, CNKI, VIP, and SinoMed(from inception to February 16, 2022). RevMan 5.3 and Stata 15.0 were employed for data analysis. Finally, 53 RCTs, involving 4 280 patients were included. The experimental groups involved the following injections: including Danshen Chuanxiongqin Injection, Tanshinone Ⅱ_A Sodium Sulfonate Injection, Danhong Injection, Dengzhan Xixin Injection, Gugua Extract Injection, Honghua Injection, Lugua Polypeptide Injection, Lugua Polypeptide Injection + Tanshinone Ⅱ_A Sodium Sulfonate Injection, Shuxuetong Injection, Zhengqing Fengtongning Injection, Compound Danshen Injection, and Xuebijing Injection. The network Meta-analysis showcased the following trends.(1) As for improving total clinical effective rate, the surface under the cumulative ranking curve(SUCRA) followed the order of conventional treatment of western medicine combined with Xuebijing Injection > combined with Gugua Extract Injection > combined with Compound Danshen Injection > combined with Danshen Chuanxiongqin Injection > combined with Honghua Injection > combined with Zhengqing Fengtongning Injection > combined with Danhong Injection > combined with Lugua Polypeptide Injection > combined with Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Dengzhan Xixin Injection.(2) As for improving erythrocyte sedimentation rate(ESR), SUCRA followed the order of conventional treatment of western medicine combined with Xuebijing Injection > combined with Shuxuetong Injection > combined with Honghua Injection > combined with Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Gugua Extract Injection > combined with Danhong Injection > combined with Lugua Polypeptide Injection > combined with Dengzhan Xixin Injection > combined with Lugua Polypeptide Injection + Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Danshen Chuanxiongqin Injection > combined with Zhengqing Fengtongning Injection.(3) As for improving rheumatoid factor(RF), SUCRA followed the order of conventional treatment of western medicine combined with Lugua Polypeptide Injection > combined with Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Lugua Polypeptide Injection + Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Gugua Extract Injection > combined with Danshen Chuanxiongqin Injection > combined with Zhengqing Fengtongning Injection > combined with Danhong Injection > combined with Dengzhan Xixin Injection.(4) As for improving C-reactive protein(CRP), SUCRA followed the order of conventional treatment of western medicine combined with Xuebijing Injection > combined with Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Lugua Polypeptide Injection + Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Honghua Injection > combined with Danshen Chuanxiongqin Injection > combined with Dengzhan Xixin Injection > combined with Gugua Extract Injection > combined with Lugua Polypeptide Injection > combined with Zhengqing Fengtongning Injection > combined with Danhong Injection.(5) As for alleviating morning stiffness, SUCRA followed the order of conventional treatment of western medicine combined with Shuxuetong Injection > combined with Lugua Polypeptide Injection > combined with Dengzhan Xixin Injection > combined with Xuebijing Injection > combined with Gugua Extract Injection > combined with Zhengqing Fengtongning Injection > combined with Danhong Injection > combined with Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Honghua Injection.(6) As for improving disease activity score(DAS28), SUCRA followed the order of conventional treatment of western medicine combined with Lugua Polypeptide Injection + Tanshinone Ⅱ_A Sodium Sulfonate Injection > combined with Lugua Polypeptide Injection > combined with Zhengqing Fengtongning Injection > combined with Honghua Injection > combined with Gugua Extract Injection > combined with Dengzhan Xixin Injection. The experimental groups had lower incidence of adverse reactions than the control group. The results of network Meta-analysis suggest that on the combination of conventional treatment of western medicine with Chinese medicine injections can improve the efficacy on rheumatoid arthritis. However, in view of the great differences in the quality and number of studies included for different therapies, the SUCRA of Chinese medicine injections need to be further verified with high-quality multi-center, large-sample, randomized double-blind trials.

Positive and negative regulation of transferred nif genes mediated by indigenous GlnR in Gram-positive Paenibacillus polymyxa.

Ammonia is a major signal that regulates nitrogen fixation in most diazotrophs. Regulation of nitrogen fixation by ammonia in the Gram-negative diazotrophs is well-characterized. In these bacteria, this regulation occurs mainly at the level of nif (nitrogen fixation) gene transcription, which requires a nif-specific activator, NifA. Although Gram-positive and diazotrophic Paenibacilli have been extensively used as a bacterial fertilizer in agriculture, how nitrogen fixation is regulated in response to nitrogen availability in these bacteria remains unclear. An indigenous GlnR and GlnR/TnrA-binding sites in the promoter region of the nif cluster are conserved in these strains, indicating the role of GlnR as a regulator of nitrogen fixation. In this study, we for the first time reveal that GlnR of Paenibacillus polymyxa WLY78 is essentially required for nif gene transcription under nitrogen limitation, whereas both GlnR and glutamine synthetase (GS) encoded by glnA within glnRA operon are required for repressing nif expression under excess nitrogen. Dimerization of GlnR is necessary for binding of GlnR to DNA. GlnR in P. polymyxa WLY78 exists in a mixture of dimers and monomers. The C-terminal region of GlnR monomer is an autoinhibitory domain that prevents GlnR from binding DNA. Two GlnR-biding sites flank the -35/-10 regions of the nif promoter of the nif operon (nifBHDKENXhesAnifV). The GlnR-binding site Ⅰ (located upstream of -35/-10 regions of the nif promoter) is specially required for activating nif transcription, while GlnR-binding siteⅡ (located downstream of -35/-10 regions of the nif promoter) is for repressing nif expression. Under nitrogen limitation, GlnR dimer binds to GlnR-binding siteⅠ in a weak and transient association way and then activates nif transcription. During excess nitrogen, glutamine binds to and feedback inhibits GS by forming the complex FBI-GS. The FBI-GS interacts with the C-terminal domain of GlnR and stabilizes the binding affinity of GlnR to GlnR-binding site Ⅱ and thus represses nif transcription.

The Role of Fnr Paralogs in Controlling Anaerobic Metabolism in the Diazotroph Paenibacillus polymyxa WLY78.

Fnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1, fnr3, fnr5, and fnr7) coding for Fnr proteins in Paenibacillus polymyxa WLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity with Bacillus cereus Fnr and Bacillus subtilis Fnr in sequence and structures. Both the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 in Escherichia coli could bind to the specific DNA promoter. Deletion analysis showed that the four fnr genes, especially fnr1 and fnr3, have significant impacts on growth and nitrogenase activity. Single deletion of fnr1 or fnr3 led to a 50% reduction in nitrogenase activity, and double deletion of fnr1 and fnr3 resulted to a 90% reduction in activity. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression of nif (nitrogen fixation) genes and Fe transport genes under anaerobic conditions. Fnr1 and Fnr3 inhibited expression of the genes involved in the aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes.IMPORTANCE The members of the nitrogen-fixing Paenibacillus spp. have great potential to be used as a bacterial fertilizer in agriculture. However, the functions of the fnr gene(s) in nitrogen fixation and other metabolisms in Paenibacillus spp. are not known. Here, we found that in P. polymyxa WLY78, Fnr1 and Fnr3 were responsible for regulation of numerous genes in response to changes in oxygen levels, but Fnr5 and Fnr7 exhibited little effect. Fnr1 and Fnr3 indirectly or directly regulated many types of important metabolism, such as nitrogen fixation, Fe uptake, respiration, and electron transport. This study not only reveals the function of the fnr genes of P. polymyxa WLY78 in nitrogen fixation and other metabolisms but also will provide insight into the evolution and regulatory mechanisms of fnr in Paenibacillus.

Development and validation of a multimodal feature fusion prognostic model for lumbar degenerative disease based on machine learning: a study protocol.

INTRODUCTION: Lumbar degenerative disease (LDD) is one of the most common reasons for patients to present with low back pain. Proper evaluation and treatment of patients with LDD are important, which clinicians perform using a variety of predictors for guidance in choosing the most appropriate treatment. Because evidence on which treatment is best for LDD is limited, the purpose of this study is to establish a clinical prediction model based on machine learning (ML) to accurately predict outcomes of patients with LDDs in the early stages by their clinical characteristics and imaging changes. METHODS AND ANALYSIS: In this study, we develop and validate a clinical prognostic model to determine whether patients will experience complications within 6 months after percutaneous endoscopic lumbar discectomy (PELD). Baseline data will be collected from patients' electronic medical records. As of now, we have recruited a total of 580 participants (n=400 for development, n=180 for validation). The study's primary outcome will be the incidence of complications within 6 months after PELD. We will use an ML algorithm and a multiple logistic regression analysis model to screen factors affecting surgical efficacy. We will evaluate the calibration and differentiation performance of the model by the area under the curve. Sensitivity (Sen), specificity, positive predictive value and negative predictive value will be reported in the validation data set, with a target of 80% Sen. The results of this study could better illustrate the performance of the clinical prediction model, ultimately helping both clinicians and patients. ETHICS AND DISSEMINATION: Ethical approval was obtained from the medical ethics committee of the Affiliated Hospital of Gansu University of Traditional Chinese Medicine (Lanzhou, China; No. 2022-57). Findings and related data will be disseminated in peer-reviewed journals, at conferences, and through open scientific frameworks. TRIAL REGISTRATION NUMBER: Chinese Clinical Trial Register (www.chictr.org.cn) No. ChiCTR2200064421.

Use self-gravitation traction to treat lumbar disc herniation: Study protocol for a double-center, single-blind randomized controlled trial.

BACKGROUND: Self-gravitation traction is 1 of the most popular treatments for lumbar disc herniation (LDH). This study aims to evaluate the effectiveness and safety of the self-gravitation traction device in the treatment of LDH and to confirm its positive treatment effect. METHODOLOGY: This trial is designed as a pragmatic double-center, single-blind, and 3-arm (1:1:1 ratio) randomized controlled trial. The recruited patients with LDH will be randomly allocated to the intervention (traction weight is 40% or 60% of its body weight) or control (traction weight is 20% of its body weight) group. Traction will be completed within 6 consecutive weeks (3 times a week), with 10 minutes of traction for the first 3 weeks, 20 minutes of traction for the next 3 weeks. After the experiment is completed, we will establish an experiment-related database. The software of SPSS, version 21 (SPSS Inc. Chicago, IL) will be used for statistical analysis, and measurement data will be expressed via mean and standard deviation (mean ±â€…SD). DISCUSSION: Once the trial is completed, we will publish the study in journals in both Chinese and English to promote the dissemination and use of the results. In addition, we also plan to promote the research results at various academic conferences both domestically and internationally.

Effects of Baduanjin on postoperative rehabilitation of patients with breast cancer: A protocol for systematic review and meta-analysis.

BACKGROUND: Baduanjin, as an ancient Chinese exercise, is beneficial to both physical and mental health. Moreover, researchers discovered that Baduanjin has effects on the recovery of postoperative breast cancer patients. Yet, nobody focused on the systematic review, which can provide convincing evidence to verify the effect of Baduanjin in breast cancer patients. Therefore, our study will conduct a systematic review to fill in the blank, besides we will offer new evidence for clinical workers. METHODS: PubMed, Embase.com, the Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, China National Knowledge Infrastructure (CNKI), Wanfang, and SinoMed will be used for literature search, retrieve time is up to June 1, 2021. We will include randomized controlled trials that evaluate the effects of Baduanjin on postoperative rehabilitation for breast cancer patients. Two independent researchers will perform study selection and data extraction. The risk of bias will be assessed by the Cochrane bias assessment tool. We will use funnel plot and Egger test to evaluate publication bias. Stata 13.0, as a necessary software, will be used to perform statistical analysis. Also, we will utilize subgroup analyses and sensitivity analyses to explore the sources of heterogeneity. RESULTS: The results of this study will be published in a peer-reviewed journal. CONCLUSION: Evidence that adequately assesses the effect of Baduanjin in the recovery of breast cancer patients will be confirmed through this systematic review. Our study will offer a guideline for clinical workers, besides we will supply a new way for the rehabilitation of breast cancer patients.

Compound kushen injection for multiple myeloma: A protocol of systematic review and meta-analysis.

BACKGROUND: Compound kushen injection is increasingly used to treat various cancers. However, its role in the management of multiple myeloma (MM) is still controversial and requires further clarification. The aim of this study is to evaluate efficacy and safety of compound kushen injection for MM through systematic review and meta-analysis. METHODS: We are going to search the 6 electronic databases: PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure, Wangfang and Chinese Biomedical Literature Database. General characteristics and Specific trial characteristics will be collected from the included studies. The outcomes included overall response rate, complete response rate, 3-year progression-free survival rate, 3-year overall survival rate, and different types of treatment-related adverse events. We calculated the risk ratios as well as their 95% confidence intervals of these outcomes and pooled the results through RevMan 5.2 software. DISCUSSION: The results of the study will be submitted to a peer-reviewed journal for publication. ETHICS AND DISSEMINATION: This study is not a clinical study, ethical approval is not required.

Suppression of hesA mutation on nitrogenase activity in Paenibacillus polymyxa WLY78 with the addition of high levels of molybdate or cystine.

The diazotrophic Paenibacillus polymyxa WLY78 possesses a minimal nitrogen fixation gene cluster consisting of nine genes (nifB nifH nifD nifK nifE nifN nifX hesA and nifV). Notably, the hesA gene contained within the nif gene cluster is also found within nif gene clusters among diazotrophic cyanobacteria and Frankia. The predicted product HesA is a member of the ThiF-MoeB-HesA family containing an N-terminal nucleotide binding domain and a C-terminal MoeZ/MoeB-like domain. However, the function of hesA gene in nitrogen fixation is unknown. In this study, we demonstrate that the hesA mutation of P. polymyxa WLY78 leads to nearly complete loss of nitrogenase activity. The effect of the mutation can be partially suppressed by the addition of high levels of molybdate or cystine. However, the nitrogenase activity of the hesA mutant could not be restored by Klebsiella oxytoca nifQ or Escherichia coli moeB completely. In addition, the hesA mutation does not affect nitrate reductase activity of P. polymyxa WLY78. Our results demonstrate hesA is a novel gene specially required for nitrogen fixation and its role is related to introduction of S and Mo into the FeMo-co of nitrogenase.

Percutaneous endoscopic decompression for lumbar spinal stenosis: Protocol for a systematic review and network meta-analysis.

BACKGROUND: Lumbar spinal stenosis (LSS) is a common and frequently-occurring disease in clinical practice. There are many interventions to treat it, and percutaneous endoscopic decompression (PED) is one of them, but their relative efficacy and safety remains unclear. Hence, the present study aims to synthesize the available direct and indirect evidence on the PED and other treatments for LSS. METHODS: The following databases will be searched: Cochrane Library, PubMed, Web of Science, Embase and China Biomedical Literature Database (CBM). The search dates will be set from the inception to April 2019. All randomized controlled trials (RCTs) will be included in this network meta-analysis (NMA) and their risk of bias will be assessed using Cochrane handbook tool by 2 independent authors. The efficacy outcomes including: Back and Leg Visual Analog Scale (VAS) score, MacNab criteria, the Oswestry Disability Index (ODI), and Japanese Orthopedic Association (JOA) score. The safety outcomes including: incidence of complications (dura tear, incomplete decompression, reoperation, etc.). A network meta-analysis will be performed using R x64 3.5.1 software and pairwise meta-analysis will be conducted using Stata 12.0 software. Grading of recommendations assessment, development, and evaluation (GRADE) will be used to assess evidence quality. RESULTS: The results of NMA will be submitted to a peer-reviewed journal. CONCLUSION: The NMA will provide a comprehensive evidence summary on treatments for patients with LSS. PROTOCOL REGISTRATION NUMBER: CRD42019120509.

Therapies of varicose veins: Protocol for the reporting and methodological quality of pairwise meta-analyses.

BACKGROUND: Many pairwise meta-analyses (MAs) related to therapies of varicose veins have been published, but their reporting and methodological quality remain unclear. The present study was designed to assess the overall quality of pairwise MAs related to therapies of varicose veins. METHODS: We will systematically search 4 electronic databases, including PubMed, EMBASE, Cochrane Library, Chinese Biomedical Database, to identify pairwise MAs related to therapies of varicose veins. The search time-span was set from inception to March 2019. The pairwise MAs related to therapies of varicose veins will be included in our overview. The reporting and methodological quality of included MAs will be assessed using preferred reporting items for systematic review and meta-analysis and a measurement tool to assess systematic reviews 2, respectively. Meanwhile, we will extract some general characteristics of included MAs, including first author; published year, journal, sample size, number of studies, number of randomized controlled trials and intervention details, and so on. All literatures screening, quality assessment, and data extraction will be independently completed by 2 of all reviewers, and any disagreement will be resolved by discussion. Besides, an increasingly popular method - evidence mapping, will be used to present the whole evidence landscape related to therapies of varicose veins. The assessment results will be presented as percentage and event/total. The Excel 2016 will be used to manage and analyze data. RESULTS: The results of the overview will be submitted to a peer-reviewed journal for publication. CONCLUSION: This overview will summarize the overall reporting and methodological quality related to therapies of varicose veins. PROSPERO REGISTRATION NUMBER: CRD42019126722.