Investigating the success of Acinetobacter baumannii in the clinical setting

Acinetobacter baumannii is an increasingly problematic hospital-associated opportunistic human pathogen that causes a range of infections such as respiratory, urinary tract and blood infections. The ability of nosocomial A. baumannii isolates to resist a diverse range of antimicrobial compounds and persist in clinical settings makes it a growing public health problem. Multidrug efflux pumps are significant contributors to antimicrobial resistance determinant in this microorganism. Five multidrug efflux pump superfamilies have been well described in bacteria, and characterized representatives of each of these five families are found in A. baumannii. In addition to drug efflux pumps and other resistance determinants, the capability of this pathogen to flourish in mixed species biofilm communities contributes to its success in the clinical setting. Recently, AceI from A. baumannii has been shown to be a novel chlorhexidine efflux pump. In this study, 23 homologs of aceI from different bacteria were cloned and expressed, and many of the homologs were found to confer resistance to additional biocides, including benzalkonium, dequalinium, proflavine, and acriflavine. Fluorimetric transport assays indicated that an AceI homolog from Vibrio parahaemolyticus mediated resistance to proflavine and acriflavine via an active efflux mechanism. Thus, this group of AceI homologs represent a new multidrug efflux protein family, the proteobacterial antimicrobial compound efflux (PACE) family. This is the first new multidrug efflux family to be found in the past 15 years. The function of AceR, a putative LysR family transcriptional regulator located adjacent to aceI in the A. baumannii genome, was investigated. AceR was demonstrated to be an activator of aceI gene expression, and induction is responsive to the AceI substrate chlorhexidine. AceR was demonstrated to bind in a chlorhexidine-inducible manner with a region of DNA upstream of the putative aceI promoter. AceR represents the first regulator of a PACE family pump to be functionally characterized. A novel high-throughput screening approach was developed to identify genes encoding multidrug efflux pumps and regulators in A. baumannii. This innovative screening method combines fluorescence-activated cell sorting (FACS) in parallel with transposon directed insertion sequencing (TraDIS). The feasibility of this method was demonstrated using a population of more than 100,000 random mutants shocked with ethidium bromide, a common substrate of multidrug efflux pumps. Ethidium bromide is differentially fluorescent inside and outside the bacterial cytoplasm due to its ability to bind nucleic acids. Cells containing the highest and the lowest concentrations of ethidium were collected, as the fluorescence intensity of the mutant cells can be distinguished by FACS. TraDIS was then applied to determine the genomic locations of transposon insertion within the collected mutants. AdeABC, AdeIJK, and AmvA efflux proteins were identified as the major ethidium efflux systems in A. baumannii, and a new transcriptional regulator that controls amvA expression was identified. Another aspect of this work focused on clinical strains of A. baumannii and Klebsiella pneumoniae isolated from a respiratory tract infection from a single patient. Co-culture studies of these two pathogens showed complex, multifaceted interactions that were dependent on their growth state and media. Metabolic profiling showed that the two pathogens had very different carbon utilization capabilities, and cross-feeding studies indicated that A. baumannii was able to utilize a secreted metabolite from K. pneumoniae as a sole carbon source. Transcriptomic analysis of the two strains co-grown in a biofilm identified significant changes in the expression levels of genes encoding surface structure biogenesis, amino acid catabolism and transport, as well as biofilm formation. Overall, this thesis provides new insight into the function and regulation of a novel class of multidrug efflux pumps, enabled the development of a new approach for identifying drug efflux pumps and their regulators, and provides a first look at the molecular and physiological interactions of two co-isolated pathogens

Identification of macrophage-related molecular subgroups and risk signature in colorectal cancer based on a bioinformatics analysis

Macrophages play a crucial role in tumor initiation and progression, while macrophage-associated gene signature in colorectal cancer (CRC) patients has not been investigated. Our study aimed to identify macrophage-related molecular subgroups and develop a macrophage-related risk model to predict CRC prognosis. The mRNA expression profile and clinical information of CRC patients were obtained from TCGA and GEO databases. CRC patients from TCGA were divided into high and low macrophage subgroups based on the median macrophage score. The ESTIMATE and CIBERSORT algorithms were used to assess immune cell infiltration between subgroups. GSVA and GSEA analyses were performed to investigate differences in enriched pathways between subgroups. Univariate and LASSO Cox regression were used to build a prognostic risk model, which was further validated in the GSE39582 dataset. A high macrophage score subgroup was associated with poor prognosis, highly activated immune-related pathways and an immune-active microenvironment. A total of 547 differentially expressed macrophage-related genes (DEMRGs) were identified, among which seven genes (including RIMKLB, UST, PCOLCE2, ZNF829, TMEM59L, CILP2, DTNA) were identified by COX regression analyses and used to build a risk score model. The risk model shows good predictive and diagnostic values for CRC patients in both TCGA and GSE39852 datasets. Furthermore, multivariate Cox regression analysis showed that the risk score was an independent risk factor for overall survival in CRC patients. Our findings provided a novel insight into macrophage heterogeneity and its immunological role in CRC. This risk score model may serve as an effective prognostic tool and contribute to personalised clinical management of CRC patients.</p

Simple Conversion of Aromatic Amines into Azides

A straightforward and highly efficient synthesis of aromatic azides from the corresponding amines is accomplished using triflyl azide under mild conditions

Wireless sensor network model.

Aiming at the quantum algorithm which can solve the problem of large integer decomposition and discrete logarithm in polynomial time, an anti-quantum computing key management scheme for clustered sensor networks is proposed in this paper. The lattice-based cryptosystem is used to achieve the anti-quantum performance of the key management scheme, and the security of the network is further improved through the mutual authentication of sensor network nodes. Due to the limited storage space of sensor nodes, this paper adopts the cluster management of wireless sensor networks, and most sensor nodes only need a small amount of storage space, thus reducing the deployment cost. Cluster management is suitable for medium and large-scale deployment of sensor networks. Because the data traffic is much larger than that of mutual authentication, the sensor nodes in wireless sensor networks use symmetric keys to communicate with each other after mutual authentication, which can effectively improve the communication efficiency in the case of frequent data communication. Experiments show that the authentication scheme based on lattice cryptosystem proposed in this paper will not improve with the continuous improvement of the security level, and its authentication scale will maintain a relatively stable state, while the algorithm scheme based on RSA will increase the authentication cost with the continuous improvement of the security level, so the scheme proposed in this paper is more suitable for application in the environment with high security level. This scheme can effectively reduce the cost of mutual authentication of sensor nodes, is conducive to the expansion of the network, and can ensure the security of authentication between sensor nodes even in the post-quantum era.</div

Comparison with RSA and ECC algorithms.

Aiming at the quantum algorithm which can solve the problem of large integer decomposition and discrete logarithm in polynomial time, an anti-quantum computing key management scheme for clustered sensor networks is proposed in this paper. The lattice-based cryptosystem is used to achieve the anti-quantum performance of the key management scheme, and the security of the network is further improved through the mutual authentication of sensor network nodes. Due to the limited storage space of sensor nodes, this paper adopts the cluster management of wireless sensor networks, and most sensor nodes only need a small amount of storage space, thus reducing the deployment cost. Cluster management is suitable for medium and large-scale deployment of sensor networks. Because the data traffic is much larger than that of mutual authentication, the sensor nodes in wireless sensor networks use symmetric keys to communicate with each other after mutual authentication, which can effectively improve the communication efficiency in the case of frequent data communication. Experiments show that the authentication scheme based on lattice cryptosystem proposed in this paper will not improve with the continuous improvement of the security level, and its authentication scale will maintain a relatively stable state, while the algorithm scheme based on RSA will increase the authentication cost with the continuous improvement of the security level, so the scheme proposed in this paper is more suitable for application in the environment with high security level. This scheme can effectively reduce the cost of mutual authentication of sensor nodes, is conducive to the expansion of the network, and can ensure the security of authentication between sensor nodes even in the post-quantum era.</div

Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability

Microsatellite instability (MSI) is a frequent and clinically relevant molecular phenotype in colorectal cancer. MSI cancers have favorable survival compared with microsatellite stable cancers (MSS), possibly due to the pronounced tumor-infiltrating lymphocytes observed in MSI cancers. Consistent with the strong immune response that MSI cancers trigger in the host, previous transcriptome expression studies have identified mRNA signatures characteristic of immune response in MSI cancers. However, proteomics features of MSI cancers and the extent to which the mRNA signatures are reflected at the protein level remain largely unknown. Here, we performed a comprehensive comparison of global proteomics profiles between MSI and MSS colorectal cancers in The Cancer Genome Atlas (TCGA) cohort. We found that protein signatures of MSI are also associated with increased immunogenicity. To reliably quantify post-transcription regulation in MSI cancers, we developed a resampling-based regression method by integrative modeling of transcriptomics and proteomics data sets. Compared with the popular simple method, which detects post-transcriptional regulation by either identifying genes differentially expressed at the mRNA level but not at the protein level or vice versa, our method provided a quantitative, more sensitive, and accurate way to identify genes subject to differential post-transcriptional regulation. With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers

Data_Sheet_1_Characteristics of cognitive function in patients with cerebellar infarction and its association with lesion location.docx

Objective: This study aimed to explore the characteristics of cognitive function in patients with cerebellar infarction and its association with lesion location.Methods: Forty-five patients with isolated cerebellar infarction were collected in the Department of Neurology, Beijing Tiantan Hospital. Thirty healthy controls were recruited matched by age and education. Global cognitive function was evaluated by using Addenbrooke’s Cognitive Examination version III (ACE-III). An extensive neuropsychological assessment battery was also tested to evaluate the characteristics of each cognitive domain. 3D slicer software was used to draw the lesion, and evaluate the lesions’ volume, side, and location. Group analysis was used to compare the differences in cognitive performance between patients and healthy controls, and patients with left and right cerebellar hemisphere infarction. Spearman analysis was used to explore the correlation between cognitive function and lesion volume. We also subdivided each patient’s lesions according to the cerebellar atlas to identify the specific cerebellar location related to cognitive decline.Results: Patients with cerebellar infarction had a lower ACE-III score compared with the healthy group (87.9 ± 6.2 vs. 93.7 ± 2.9, p Conclusion: We identified that cerebellar involvement in cognition, especially in attention processing and executive function. Cerebellar right-sided lateralization of cognition and functional topography were also revealed in the current study.</p

Down-regulated HSA_circ_0003528 inhibits hepatocellular carcinoma aggressiveness via the miR-212-3p/<i>XIAP</i> axis

Hepatocellular carcinoma (HCC) is characterized by a high mortality rate. Dysregulated circular RNAs (circRNAs) play a vital role in HCC. We aimed to study the role of circ_0003528 in HCC and its fundamental molecular mechanisms. HSA_circ_0003528 was identified through bioinformatics dataset analysis. The binding sites between mRNA and miRNA were predicted using online bioinformatics tools. The interaction between miR-212-3p and X-linked inhibitor of apoptosis protein (XIAP) or circ_0003528 was confirmed through the luciferase reporter assay. RT-qPCR and western blot assays were used to analyze the expression of all miRNAs/mRNAs and proteins. Cellular functions were evaluated using the MTT and TUNEL assays. A xenograft model was established to evaluate the function of circ_0003528 in vivo. Circ_0003528 was dramatically overexpressed in HepG2 and HUH7 cells. However, knockdown of circ_0003528 suppressed the aggressiveness of HCC cells and tumor growth both in vitro and in vivo. Furthermore, binding of miR-212-3p to circ_0003528 and XIAP was verified. Downregulation of miR-212-3p abrogated the effects of si-circ_0003528 on cell viability and apoptosis, and upregulation of XIAP antagonized the functions of the miR-212-3p mimic in HCC cells. circ_0003528 contributes to the development of HCC in vitro and in vivo via the miR-212-3p/XIAP axis. Hence, circ_0003528 knockdown may be a potential therapeutic strategy for HCC treatment.</p

Drug indication resources.

<p>Drug indication resources.</p