ggVennDiagram: Intuitive Venn diagram software extended.

Highlights of ggVennDiagram include: (1) Subset/Region filling Venn diagram up to seven sets; (2) Upset plot with unlimited sets; (3) Venn Calculator for two or more sets; (4) Provide as R package, Shiny App, and TBtools plugin.

An Approach to Constructing Multispecies Biofilm Communities from Rhizosphere Soil.

The multispecies biofilm is a naturally occurring and dominant lifestyle of bacteria in nature, including in rhizosphere soil, although the current understanding of it is limited. Here, we provide an approach to rapidly establish synergistic multispecies biofilm communities. The first step is to extract cells from rhizosphere soil using the differential centrifugation method. Afterward, these soil cells are inoculated into the culture medium to form pellicle biofilm. After 36 h of incubation, the bacterial composition of the biofilm and the solution underneath are determined using the 16S rRNA gene amplicon sequencing method. Meanwhile, high-throughput bacterial isolation from pellicle biofilm is conducted using the limiting dilution method. Then, the top 5 bacterial taxa are selected with the highest abundance in the 16S rRNA gene amplicon sequencing data (pellicle biofilm samples) for further use in constructing multispecies biofilm communities. All combinations of the 5 bacterial taxa were quickly established using a 24-well plate, selected for the strongest biofilm formation ability by the crystal violet staining assay, and quantified by qPCR. Finally, the most robust synthetic bacterial multispecies biofilm communities were obtained through the methods above. This methodology provides informative guidance for conducting research on rhizosphere multispecies biofilm and identifying representative communities for studying the principles governing interactions among these species.

Underlying anti-cancer mechanisms of histone deacetylase (HDAC) inhibitors in tamoxifen-resistant breast cancer cells.

Objectives: Breast cancer is an important women's malignancy with high cancer-related deaths worldwide. Drug resistance lowers the treatment efficacy in this malignancy. This study aimed to explore the underlying mechanisms of histone deacetylase (HDAC) inhibitor trichostatin A (TSA) to overcome resistance to tamoxifen in breast cancer cells. Materials and Methods: Tamoxifen-resistance in MCF-7 breast cancer cells was simulated. MTT assay was used to detect the cytotoxic effects of HDAC inhibitor and PI3K inhibitor on the cancer cells. Trans-well assay was applied to evaluate the invasion and migration of the treated cancer cells. Flow cytometer assay was also applied to evaluate cell cycle phases in the treated cancer cells. Finally, expression of vascular endothelial growth factor (VEGF), E-cadherin, Vimentin, phosphorylated phosphatidylinositol kinase (p-PI3k), phosphorylated protein kinase B (p-AKT), and phosphorylated mammalian target protein of rapamycin (p-mTOR) was evaluated by western blotting. Results: The obtained results indicated that HDAC inhibitor treatments significantly decreased viability, migration, and invasion in the cancer cells. Furthermore, the frequency of the treated cancer cells significantly increased in the S phase as well as significantly decreasing in the G2/M phase of the cell cycle. Moreover, HDAC inhibitor modified levels of VEGF, E-cadherin, Vimentin, p-PI3k, p-AKT, and p-mTOR proteins. However, HDAC inhibitor combined with PI3K inhibitor exerts more profound effects on the cancer cells as compared to HDAC inhibitor monotherapy. Conclusion: HDAC inhibitors inhibited the survival of breast cancer drug-resistant cells, invasion, migration, and angiogenesis by inhibiting the PI3k/Akt/mTOR signaling pathway.

SdrR, a LysR-type regulator, responds to the mycobacterial antioxidant defense.

Protection against oxidative stress is a vital defense mechanism for Mycobacterium tuberculosis within the host. However, few transcription factors that control bacterial antioxidant defense are known. Here, we present evidence that SdrR, encoded by the MSMEG_5712 (Ms5712) gene, functions as an oxidative stress response regulator in Mycobacterium smegmatis. SdrR recognizes an 11-bp motif sequence in the operon's upstream regulatory region and negatively regulates the expression of short-chain dehydrogenases/reductases (SDR). Overexpressing sdrR inhibited SDR expression, which rendered the strain oxidative more stress-sensitive. Conversely, sdrR knockout alleviates SDR repression, which increases its oxidative stress tolerance. Thus, SdrR responds to oxidative stress by negatively regulating sdr expression. Therefore, this study elucidated an underlying regulatory mechanism behind mycobacterial oxidative stress adaptation.

Constructing a CdS QDs/silica gel composite with high photosensitivity and prolonged recyclable operability for enhanced visible-light-driven NADH regeneration.

Visible-light-driven nicotinamide adenine dinucleotide (NADH) regeneration is one of the most effective measures, and cadmium sulfide (CdS) materials are typically used as low-cost photocatalysts. The CdS photocatalysts, however, still suffer from low regeneration efficiency and poor cycle stability. In this work, the CdS quantum dots (QDs) less than 10 nm embedded onto silica gel (CdS QDs/Silica gel) were constructed for visible-light-driven NADH regeneration by a successive ionic layer adsorption reaction and ball milling method. Results demonstrate that the photosensitivity of the CdS QDs/Silica gel composite was 31 times higher than that of the bulk CdS. Moreover, the conduction band (CB) edge of the CdS QDs/Silica gel composite is -1.34 eV, which is more negative 0.5 eV than that of the bulk CdS. The obtained CdS QDs/Silica gel composites showed the highest NADH regeneration yields of 68.8% under visible-light (LED, 420 nm) illumination and can be reused for over 40 cycles. Finally, the bioactivity of NADH toward enzyme catalysis is further confirmed by the hydrogenation of benzaldehyde to benzyl alcohol catalyzed with an alcohol dehydrogenase as enzyme catalysis.

Cooperative microbial interactions drive spatial segregation in porous environments.

The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.

The state and consideration for skin test of ß-lactam antibiotics in pediatrics.

ß-lactam antibiotics are the most frequently used drugs and the most common drugs that cause allergic reactions in pediatrics. The occurrence of some allergic reactions can be predicted by skin testing, especially severe adverse reactions such as anaphylactic shock. Thus, penicillin and cephalosporin skin tests are widely used to predict allergic reactions before medication in pediatrics. However, false-positive results from skin tests were more often encountered in pediatrics than in adults. In fact, many children labeled as allergic to ß-lactam are not allergic to the antibiotic, leading to the use of alternative antibiotics, which are less effective and more toxic, and the increase of antibiotic resistance. There has been controversy over whether ß-lactam antibiotics should be tested for skin allergies before application in children. Based on the great controversy in the implementation of ß-lactam antibiotic skin tests, especially the controversial cephalosporin skin tests in pediatrics, the mechanism and reasons of anaphylaxis to ß-lactam antibiotics, the significance of ß-lactam antibiotic skin tests, the current state of ß-lactam antibiotic skin tests at home and abroad, and the problems of domestic and international skin tests were analyzed to determine a unified standard of ß-lactam antibiotic skin tests in pediatrics to prevent and decrease adverse drug reactions, avoid waste of drugs, and a large amount of manpower and material resource consumption.

Extracellular polymeric substances and mineral interfacial reactions control the simultaneous immobilization and reduction of arsenic (As(V)).

Extracellular polymeric substances (EPS) play a crucial role in controlling the mobility and bioavailability of heavy metal(loid)s in water, soils, and sediments. The formation of EPS-mineral complex changes the reactivity of the end-member materials. However, little is known about the adsorption and redox mechanisms of arsenate (As(V)) in EPS and EPS-mineral complexes. Here we examined the reaction sites, valence state, thermodynamic parameters and distribution of As in the complexes using potentiometric titration, isothermal titration calorimetry (ITC), FTIR, XPS, and SEM-EDS. The results showed that ∼54% of As(V) was reduced to As(III) by EPS, potentially driven by an enthalpy change (ΔH) of - 24.95 kJ/mol. The EPS coating on minerals clearly affected the reactivity to As(V). The strong masking of functional sites between EPS and goethite inhibited both the adsorption and reduction of As. In contrast, the weak binding of EPS onto montmorillonite retained more reactive sites for the reaction with As. Meanwhile, montmorillonite facilitated the immobilization of As to EPS through the formation of As-organic bounds. Our findings deepen the understanding of EPS-mineral interfacial reactions in controlling the redox and mobility of As, and the knowledge is important for predicting the behavior of As in natural environments.

Stronger linkage of diversity-carbon decomposition for rare rather than abundant bacteria in woodland soils.

Soil microbial diversity is important for maintaining ecosystem functions. However, the linkage between microbial diversity, especially rare and abundant bacterial diversity, and carbon decomposition remains largely unknown. In this study, we assessed the establishment and maintenance of rare and abundant bacterial α-diversities at the taxonomic and phylogenetic levels and their linkages with soil carbon decomposition separately in four Chinese woodlands. Compared to abundant bacteria, rare bacteria showed higher community diversity, tighter phylogenetic clustering, wider environmental breadth, stronger phylogenetic signals, and higher functional redundancy. The assembly of the abundant bacterial subcommunity was governed by stochastic (59.2%) and deterministic (41.8%) processes, whereas the assembly of the rare bacterial subcommunity was mainly dominated by deterministic processes (85.8%). Furthermore, total phosphorus, soil pH, and ammonium nitrogen balanced stochastic and deterministic processes in both rare and abundant bacterial subcommunities. Our results reveal that rare bacteria displayed stronger environmental adaptability and environmental constraint. Importantly, the α-diversities of rare taxa, rather than abundant taxa, were significantly related to carbon decomposition. This study provides a holistic understanding of biogeographic patterns of abundant and rare bacteria and their α-diversities in relation to carbon decomposition, thus helping us better predict and regulate carbon dynamics under the background of global climate change.

Regulation of CRISPR-Associated Genes by Rv1776c (CasR) in Mycobacterium tuberculosis.

The CRISPR-Cas system is an adaptive immune system for many bacteria and archaea to defend against foreign nucleic acid invasion, and this system is conserved in the genome of M. tuberculosis (Mtb). Although the CRISPR-Cas system-mediated immune defense mechanism has been revealed in Mtb, the regulation of cas gene expression is poorly understood. In this study, we identified a transcription factor, CasR (CRISPR-associated protein repressor, encoded by Rv1776c), and it could bind to the upstream DNA sequence of the CRISPR-Cas gene cluster and regulate the expression of cas genes. EMSA and ChIP assays confirmed that CasR could interact with the upstream sequence of the csm6 promoter, both in vivo and in vitro. Furthermore, DNA footprinting assay revealed that CasR recognized a 20 bp palindromic sequence motif and negatively regulated the expression of csm6. In conclusion, our research elucidates the regulatory effect of CasR on the expression of CRISPR-associated genes in mycobacteria, thus providing insight into gene expression regulation of the CRISPR-Cas system.

Identification and validation of circulating biomarkers for detection of liver cancer with antibody array.

The aim of this study was to find new protein biomarkers that could be used to detect hepatocellular carcinoma (HCC) in the serum. We identified 11 proteins in the tissue that could be used to classify samples from HCC and control subjects. The 11 identified tissue biomarkers were combined with 10 commonly used serum HCC biomarkers for further verification in a large number of serum samples from HCC patients and healthy controls. 17 of the 21 prospective serum biomarkers were determined to be differentially expressed through collinearity and significance analysis. Through the method of supervised learning, a random forest model was constructed to reduce the dimensionality of the number of differentially expressed proteins, and finally, 4 differentially expressed proteins were identified: AFP, GDF15, CEACAM-1, and MMP-9, and suggested to have potential application in clinical diagnosis of HCC.

The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA.

In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.

Ionic Strength-Dependent Attachment of Pseudomonas aeruginosa PAO1 on Graphene Oxide Surfaces.

Graphene oxide (GO) is a widely used antimicrobial and antibiofouling material in surface modification. Although the antibacterial mechanisms of GO have been thoroughly elucidated, the dynamics of bacterial attachment on GO surfaces under environmentally relevant conditions remain largely unknown. In this study, quartz crystal microbalance with dissipation monitoring (QCM-D) was used to examine the dynamic attachment processes of a model organism Pseudomonas aeruginosa PAO1 onto GO surface under different ionic strengths (1-600 mM NaCl). Our results show the highest bacterial attachment at moderate ionic strengths (200-400 mM). The quantitative model of QCM-D reveals that the enhanced bacterial attachment is attributed to the higher contact area between bacterial cells and GO surface. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and atomic force microscopy (AFM) analysis were employed to reveal the mechanisms of the bacteria-GO interactions under different ionic strengths. The strong electrostatic and steric repulsion at low ionic strengths (1-100 mM) was found to hinder the bacteria-GO interaction, while the limited polymer bridging caused by the collapse of biopolymer layers reduced cell attachment at a high ionic strength (600 mM). These findings advance our understanding of the ionic strength-dependent bacteria-GO interaction and provide implications to further improve the antibiofouling performance of GO-modified surfaces.

The spike-ACE2 binding assay: An in vitro platform for evaluating vaccination efficacy and for screening SARS-CoV-2 inhibitors and neutralizing antibodies.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has become a worldwide pandemic, and there is a pressing need for the rapid development of novel therapeutic strategies. SARS-CoV-2 viral entry is mediated by interaction between the receptor binding domain (RBD) of the SARS-CoV-2 Spike protein and host cellular receptor, human angiotensin converting enzyme 2 (ACE2). The lack of a high throughput screening (HTS) platform for candidate drug screening means that no targeted COVID-19 treatments have been developed to date. To overcome this limitation, we developed a novel, rapid, simple, and HTS binding assay platform to screen potential inhibitors of the RBD-ACE2 complex. Three "neutralizing" mouse monoclonal antibodies capable of blocking the RBD-ACE2 interaction were identified using our binding assay and pseudovirus neutralization assay followed by further validation with the Focus Reduction Neutralization Test (FRNT), which analyzes the neutralization capacity of samples in the presence of live SARS-CoV-2. Furthermore, the consistency of our binding assay and FRNT results (R2 = 0.68) was demonstrated by patients' serum, of which were COVID-19 positive (n = 34) and COVID-19 negative (n = 76). Several small molecules selected for their potential to inhibit the Spike-ACE2 complex in silico were also confirmed with the binding assay. In addition, we have evaluated vaccine efficacy using binding assay platform and validated through pseudovirus neutralization assay. The correlation between binding assay & psuedovirus assay of the post vaccinated serum showed well correlated (R2 = 0.09) Moreover, our binding assay platform successfully validated different Spike RBD mutants. These results indicate that our binding assay can be used as a platform for in vitro screening of small molecules and monoclonal antibodies, and high-throughput assessment of antibody levels after vaccination. When conducting drug screening, computer virtual screening lacks actual basis, construction of pseudoviruses is relatively complicated, and even FRNT requires a P3 laboratory. There are few methods to determine the competitiveness of the target drug and SRBD or ACE2. Our binding assay can fill this gap and accelerate the process and efficiency of COVID-19 drug screening.

Development of an Immunoassay Method for the Sensitive Detection of Histamine and Tryptamine in Foods Based on a CuO@Au Nanoenzyme Label and Molecularly Imprinted Biomimetic Antibody.

In this paper, a novel biomimetic enzyme-linked immunoassay method (BELISA) was successfully established for the detection of histamine and tryptamine, based on catalytically active cupric oxide@gold nanoparticles (CuO@Au NPs) as a marker and a molecularly imprinted polymer (MIP) as the biomimetic antibody. Under optimized conditions, the detection limitations of the BELISA method for histamine and tryptamine were 0.04 mg L-1 and 0.14 mg L-1, respectively. For liquor spiked with histamine and tryptamine, the BELISA method delivered satisfactory recoveries ranging from 89.90% to 115.00%. Furthermore, the levels of histamine and tryptamine in fish, soy sauce, and rice vinegar samples were detected by the BELISA method and a high performance liquid chromatography method, with no significant difference between the two methods being found. Although the catalytic activity of nanozymes is still lower than that of natural enzymes, the BELISA method could still sensitively determine the histamine and tryptamine levels in food samples.

Comprehensive analysis of competitive endogenous RNAs networks reveals potential prognostic biomarkers associated with epithelial ovarian cancer.

Ovarian cancer (OC) is a major health threat to females, as it has high morbidity and mortality. Evidence has increasingly demonstrated that long non-coding RNAs (lncRNAs) regulate OC progression and they may have value as early diagnostic biomarkers, prognostic biomarkers and/or therapeutic targets. In the present study, the regulatory mechanisms and prognosis associated with cancer-specific lncRNAs and their related competing endogenous (ce)RNA network in OC were investigated. The differential expression profiles and prognostic significance of lncRNAs and mRNAs were systematically explored based on data from 359 OC cases from The Cancer Genome Atlas and 180 healthy individuals from the Genotype-Tissue Expression database. Functional enrichment analyses, RNA-RNA interactome prediction, ceRNA network analysis, correlation analysis and survival analysis were utilized to identify hub lncRNAs and biomarkers associated with OC diagnosis or prognosis. A total of 1,049 differentially expressed lncRNAs and 6,516 differentially expressed mRNAs between OC and healthy tissues were detected. An lncRNA-micro (mi)RNA-mRNA regulatory network in OC was further established, containing 91 lncRNAs, 23 miRNAs and 179 mRNAs. After survival analysis based on the expression of the RNAs in the ceRNA network, 8 lncRNAs, 4 miRNAs and 11 mRNAs that were significantly associated with OC patient survival (P<0.05) were obtained. Using least absolute shrinkage and selection operator-penalized Cox regression, an eight-lncRNA risk score model was generated, which was able to readily discriminate between OC and healthy individuals and predict the survival of patients with OC. In addition, the differential expression of several key lncRNAs and mRNAs was verified by reverse transcription-quantitative PCR and western blot analysis. The current study presents a novel lncRNA-miRNA-mRNA network, which provides insight into the potential pathogenesis of OC and allows the identification of prognostic biomarkers and treatment strategies for OC.

Atractylenolide III alleviates sepsis-mediated lung injury via inhibition of FoxO1 and VNN1 protein.

PURPOSE: To evaluate the influence of atractylenolide (Atr) III on sepsis-induced lung damage. METHODS: We constructed a mouse sepsis model through cecal ligation and puncture. These mice were allocated to the normal, sepsis, sepsis + Atr III-L (2 mg/kg), as well as Atr III-H (8 mg/kg) group. Lung injury and pulmonary fibrosis were accessed via hematoxylin-eosin (HE) and Masson's staining. We used terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and flow cytometry for detecting sepsis-induced lung cell apoptosis. The contents of the inflammatory cytokines in lung tissue were measured via enzyme-linked immunosorbent assay (ELISA). RESULTS: Atr III-H did not only reduce sepsis-induced lung injury and apoptosis level, but also curbed the secretion of inflammatory factors. Atr III-H substantially ameliorated lung function and raised Bcl-2 expression. Atr III-H eased the pulmonary fibrosis damage and Bax, caspase-3, Vanin-1 (VNN1), as well as Forkhead Box Protein O1 (FoxO1) expression. CONCLUSIONS: Atr III alleviates sepsis-mediated lung injury via inhibition of FoxO1 and VNN1 protein.

ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram.

Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could automatically generate high-quality Venn diagrams with two to seven sets. The ggVennDiagram is built based on ggplot2, and it integrates the advantages of existing packages, such as venn, RVenn, VennDiagram, and sf. Satisfactory results can be obtained with minimal configurations. Furthermore, we designed comprehensive objects to store the entire data of the Venn diagram, which allowed free access to both intersection values and Venn plot sub-elements, such as set label/edge and region label/filling. Therefore, high customization of every Venn plot sub-element can be fulfilled without increasing the cost of learning when the user is familiar with ggplot2 methods. To date, ggVennDiagram has been cited in more than 10 publications, and its source code repository has been starred by more than 140 GitHub users, suggesting a great potential in applications. The package is an open-source software released under the GPL-3 license, and it is freely available through CRAN (https://cran.r-project.org/package=ggVennDiagram).

Efficacy and safety of anlotinib in patients with advanced malignancy: a single-center, single-arm, phase 2 trial.

BACKGROUND: For advanced tumors that lack specific oncogenic alteration and are resistant to chemotherapy, anti-angiogenesis therapy or immunotherapy or a combination of the two are the most important treatments. Anlotinib is a newly developed oral small molecule receptor tyrosine kinases inhibitor with the potency of inhibiting tumor angiogenesis. This was an open-label, single-arm, phase 2 study to validate the efficacy and safety of anlotinib in patients with various cancer types. METHODS: Patients with advanced malignancy who have failed previous therapies or lack effective treatment choices received daily oral administration of 12 mg anlotinib on days 1-14 every 3 weeks until disease progression, intolerable toxicity or physician decision. The primary endpoint was objective response rate (ORR). RESULTS: A total of 93 eligible patients with 26 different cancer types were enrolled. The overall ORR was 21.5%. The median PFS was 5.7 months and median OS was 12.0 months. The most common treatment-related AE of all grades and of grade 3 was both hypertriglyceridemia at an incidence of 40.9% and 5.4%, respectively. CONCLUSIONS: Anlotinib exhibits objective efficacy and safety in advanced malignancy and might be a possible treatment option for many types of cancer patients who have failed prior treatment and with no optimal therapy regimen.

Emergent transcriptional adaption facilitates convergent succession within a synthetic community.

Taxonomic convergence is common in bacterial communities but its underlying molecular mechanism remains largely unknown. We thus conducted a time-series transcriptional analysis of a convergent two-species synthetic community that grew in a closed broth-culture system. By analyzing the gene expression and monitoring the community structure, we found that gene expression mainly changed in the early stage, whereas community structure significantly changed in the late stage. The significant change of gene expression occurred even at the very beginning, which was designated as "0 h effect", suggesting the effect of species interaction on gene expression was inevitable. Besides, the effect of interaction on gene expression has a "population effect", which means that majority species have greater impact on gene expressions of minority species than vice versa. Furthermore, gene set enrichment analysis revealed that among a total of 63 unique pathways (occupying about 50% of all the metabolic pathways in both species), 40 (63%) were consistently suppressed, 16 (25%) were conditionally expressed, and only 7 (11%) were consistently activated. Overall, they were strictly regulated by both time and initial structures. Therefore, we proposed that microorganism responses and the induced gene expression changes play important roles in the process of community succession.