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Background: Poor sleep quality is a global public health concern. This study aimed to identify the risk factors for sleep disorders and clarify their causal effects. Methods: Data were obtained from the National Health and Nutrition Examination Survey (NHANES) and Mendelian randomization (MR)-Base databases. Baseline characteristics of individuals with and without sleep disorders were compared. A multivariate logistic regression analysis was performed to calculate the effects of each variable on sleep disorders. Causal effects of blood lead levels and hypertension on sleep disorders were assessed using MR analysis. Results: In total, 3660 individuals were enrolled in the study. The prevalence of self-reported sleep disorders was 26.21%. Serum lead level, serum mercury level, serum retinol level, prevalence of hypertension, and daily vigorous work duration were significantly higher for those in the sleep disorders group than the control group. After adjusting for various covariates, the effects of serum lead and hypertension on sleep disorders were stable from logistic regression models 1–4. MR analysis showed that blood lead levels were causally related to the risk of sleep disorders (odds ratio (OR) = 1.09, 95% confidence interval (CI) 1.01–1.17, P = 0.030). There was no causal link between elevated blood pressure and sleep disorders (OR = 0.99, 95% CI 0.94–1.04, P = 0.757). Goodness-of-fit tests and sensitivity analyses were used to verify the reliability of the results. Conclusions: Blood lead is positively and causally associated with an increased risk of sleep disorders. These findings provide a novel perspective regarding sleep protection. Taking effective measures to reduce lead exposure may significantly improve sleep health. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae pv. actinidiae (Psa), the bacterium that causes kiwifruit bacterial canker, is a common field occurrence that is difficult to control globally. Currently, exploring the resources for efficient biocontrol bacteria is a hot spot in the field. The common strategy for isolating biocontrol bacteria is to directly isolate biocontrol bacteria that can secrete diffusible antibacterial substances, most of which are members of Bacillus, Pseudomonas and Streptomycetaceae, from disease samples or soil. Here, we report a new approach by adapting the typical isolation methods of kiwifruit canker disease to identify efficient biocontrol bacteria from the branch microbiome. Using this unique approach, we isolated a group of kiwifruit biocontrol agents (KBAs) from the branch microbiome of Psa‐resistant varieties. Thirteen of these showed no antagonistic activity in vitro, which depends on the secretion of antibacterial compounds. However, they exhibited antibacterial activity via cell‐to‐cell contacts mimicked by co‐culture on agar plates. Through biocontrol tests on plants, two isolates, KBA13 and KBA19, demonstrated their effectiveness by protecting kiwifruit branches from Psa infection. Using KBA19, identified as Pantoea endophytica, as a representative, we found that this bacterium uses the type VI secretion system (T6SS) as the main contact‐dependent antibacterial weapon that acts via translocating toxic effector proteins into Psa cells to induce cell death, and that this capacity expressed by KBA19 is common to various Psa strains from different countries. Our findings highlight a new strategy to identify efficient biocontrol agents that use the T6SS to function in an antibacterial metabolite‐independent manner to control wood diseases. [ABSTRACT FROM AUTHOR]

Background: The comorbidity rate between type 2 diabetes mellitus (T2DM) and pulmonary tuberculosis (PTB) is high and imposes enormous strains on healthcare systems. However, whether T2DM is causally associated with PTB is unknown owing to limited evidence from prospective studies. Consequently, the present study aimed to clarify the genetic causality between T2DM and PTB on the basis of Mendelian randomization (MR) analysis. Methods: Genetic variants for T2DM and PTB were obtained from the IEU OpenGWAS project. The inverse variance weighted method was used as the main statistical analysis method and was supplemented with MR-Egger, weighted median, simple mode, and weighted mode methods. Heterogeneity was analyzed using Cochran's Q statistic. Horizontal pleiotropy was assessed using the MR-PRESSO global test and MR-Egger regression. Robustness of the results was verified using the leave-one-out method. Results: A total of 152 independent single-nucleotide polymorphisms (SNPs) were selected as instrumental variables (IVs) to assess the genetic causality between T2DM and PTB. Patients with T2DM had a higher risk of PTB at the genetic level (odds ratio (OR) for MR-Egger was 1.550, OR for weighted median was 1.540, OR for inverse variance weighted was 1.191, OR for simple mode was 1.629, OR for weighted mode was 1.529). There was no horizontal pleiotropy or heterogeneity among IVs. The results were stable when removing the SNPs one by one. Conclusions: This is the first comprehensive MR analysis that revealed the genetic causality between T2DM and PTB in the East Asian population. The study provides convincing evidence that individuals with T2DM have a higher risk of developing PTB at the genetic level. This offers a significant basis for joint management of concurrent T2DM and PTB in clinical practice. [ABSTRACT FROM AUTHOR]

Purpose: This study aims to identify effective ways to promote plant-based foods in quick-service restaurants by considering customers' food-related health involvement. Design/methodology/approach: This study conducted a 2 (message format: myth/fact or fact-only) × 2 (message focus: benefit- or attribute-focused) × 2 (health involvement: high or low) quasi-experimental design via a scenario-based online survey. A multivariate analysis of covariance and a bootstrapping approach were used to test the hypotheses (N = 365). Findings: The results indicated that message format and focus jointly influenced customers' perceived health consequences of plant-based foods and purchase intentions; customers' health involvement altered the two-way interaction between message format and focus; and perceived health consequences mediated the effects of message format and focus as and customers' health involvement on purchase intentions. Research limitations/implications: This study identifies the effectiveness of message format and focus in promoting plant-based foods and extends the sustainable product promotion literature by using resource matching theory and the elaboration likelihood model. Future studies should use field studies to examine how can message framing influence customers' actual behaviors when purchasing plant-based foods. Practical implications: This study can help quick-service restaurants better promote plant-based foods considering message format and focus and customers' food-related health involvement. Originality/value: This is one of only a few studies that have tested how messages containing both negative and positive information about a product could help promote plant-based foods. [ABSTRACT FROM AUTHOR]

Background: Sufficient nutrition contributes to rapid translational elongation and protein synthesis in eukaryotic cells and prokaryotic bacteria. Fast synthesis and accumulation of type III secretion system (T3SS) proteins conduce to the invasion of pathogenic bacteria into the host cells. However, the translational elongation patterns of T3SS proteins in pathogenic bacteria under T3SS-inducing conditions remain unclear. Here, we report a mechanism of translational elongation of T3SS regulators, effectors and structural protein in four model pathogenic bacteria (Pseudomonas syringae, Pseudomonas aeruginosa, Xanthomonas oryzae and Ralstonia solanacearum) and a clinical isolate (Pseudomonas aeruginosa UCBPP-PA14) under nutrient-limiting conditions. We proposed a luminescence reporter system to quantitatively determine the translational elongation rates (ERs) of T3SS regulators, effectors and structural protein under different nutrient-limiting conditions and culture durations. Results: The translational ERs of T3SS regulators, effectors and structural protein in these pathogenic bacteria were negatively regulated by the nutrient concentration and culture duration. The translational ERs in 0.5× T3SS-inducing medium were the highest of all tested media. In 1× T3SS-inducing medium, the translational ERs were highest at 0 min and then rapidly decreased. The translational ERs of T3SS regulators, effectors and structural protein were inhibited by tRNA degradation and by reduced levels of elongation factors (EFs). Conclusions: Rapid translational ER and synthesis of T3SS protein need adequate tRNAs and EFs in nutrient-limiting conditions. Numeric presentation of T3SS translation visually indicates the invasion of bacteria and provides new insights into T3SS expression that can be applied to other pathogenic bacteria. [ABSTRACT FROM AUTHOR]

Festivals attract diverse visitors to tourism sites and contribute significant solid wastes every year. One way to help customers engage in recycling at tourist attractions is to adopt an effective communication tactic using product transformation salience (PTS). To better understand the influence of PTS, the current study investigated the roles of visitors' characteristics, such as gender and age, by using PTS messages to promote recycling behavior by presenting moderation models. This study further examined the underlying psychological mechanisms to explain the effect of PTS on recycling intention by proposing a serial mediation model. The results indicated that the effects of PTS on visitors' feedback toward green messages varied when considering visitors' age and gender. In particular, women and older attendees perceive the higher green value of recycling and develop higher intentions toward engaging in recycling practices at events. The serial mediation effects of PTS → perceived green value → attitudes → intentions were also confirmed. The findings of this study contribute to the green advertising literature and provide practical suggestions to industry practitioners. [ABSTRACT FROM AUTHOR]

In a long-term symbiotic relationship between plants and pathogens, plants have evolved to harbor beneficially endophytic microbiomes, thereby conferring them the ability to resist infection by pathogens. This prompted us to establish a phytopathogen-based co-culture platform for the targeted isolation of potential biocontrol agents from plants via specific pathogen enrichment. In this study, we investigated three different phytopathogenic systems, including kiwifruit, turfgrass, and rice, and their infectious bacterial and/or fungal pathogens. By using the developed mono- or co-enrichment platform, we efficiently isolated three antimicrobial agents, including Bacillus safensis ZK-1 against Pseudomonas syringae pv. actinidiae that causes kiwifruit canker, Pseudomonas alcaligenes ZK-2 against Clarireedia paspali that causes dollar spot disease in turfgrass, and Bacillus velezensis ZK-3 against rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae and rice blast fungus Magnaporthe oryzae. We believe that the phytopathogenic co-culture and pathogen enrichment platform developed here is versatile and effective for the isolation of potential biocontrol agents with specific or broad-spectrum antimicrobial activities from plants of interest in a targeted and large-scale manner. [ABSTRACT FROM AUTHOR]

Bacteria use a variety of mechanisms, such as two‐component regulatory systems (TCSs), to rapidly sense and respond to distinct conditions and signals in their host organisms. For example, a type III secretion system (T3SS) is a key determinant of the virulence of the model plant pathogen Pseudomonas syringae and contains the TCS RhpRS as a key regulator. However, the plant‐derived compound targeting RhpRS remains unknown. Here, we report that RhpRS directly interacts with polyphenols and responds by switching off P. syringae T3SS via crosstalk with alternative histidine kinases. We identify three natural polyphenols that induce the expression of the rhpRS operon in an RhpS‐dependent manner. The presence of these three specific polyphenols inhibits the phosphatase activity of RhpS, thus suppressing T3SS activation in T3SS‐inducing conditions. The Pro40 residue of RhpS is essential to respond to these polyphenols. In addition, three non‐cognate histidine kinases cooperatively phosphorylate RhpR and antagonize the rhpS mutant phenotype. This work illustrates that plant polyphenols can directly target P. syringae RhpRS, which results in bacterial virulence being switched off via a phosphorylation‐related crosstalk. SYNOPSIS: Polyphenols inhibit the induction of the T3SS of Pseudomonas syringae through the interaction with the Pro40 residue of RhpS. Three non‐cognate histidine kinases of RhpR are involved in the signaling pathway of polyphenol‐RhpRS‐T3SS. Polyphenols directly suppress RhpS and the type III secretion system in P. syringae.The RhpS Pro40 residue is indispensable for polyphenol perception.PSPPH_5115, PSPPH_3736 and PSPPH_3550 are non‐cognate histidine kinases of RhpR. [ABSTRACT FROM AUTHOR]

Due to the cosmetic standards of food service operators, most consumers have had limited exposure to visually unappealing foods. Thus, unused ugly foods end up becoming food waste. To encourage consumers to buy ugly foods with the hope of relieving the severity of food waste, this study attempts to further verify the effectiveness of anthropomorphism in advertising. The purpose of this study is to determine whether the effectiveness of anthropomorphism varies based on the individual consumer characteristics of gender and age. Specifically, the objectives of this study are 1) to investigate whether gender interacts with anthropomorphism and 2) to identify the moderating effect of age. A total of 421 participants were hired through Amazon Mturk, and a 2 × 2 × 2 between-subjects full-factorial experimental design was used. The results suggest that anthropomorphism could be advantageous in improving consumers' purchase intentions, as well as confirm anthropomorphism's interactional effect with gender. Furthermore, this interactional effect varies across different age groups (younger vs. older). This study extends the relevant literature and provides the food service industry with insightful marketing suggestions to promote ugly foods. [ABSTRACT FROM AUTHOR]

Purpose: This study aims to investigate consumers' intention to use onsite restaurant interactive self-service technology (ORISST) using a modified value attitude-behavior model. To extend the understanding of how consumers' dining value focus could influence their intention to use ORISST, this study examines the conditional indirect effects of restaurant type (quick-service vs fine-dining) within the proposed model. Design/methodology/approach: An online survey was developed and distributed to randomly selected respondents in the USA. A total of 588 (quick-service: 295; fine-dining: 293) responses were used for the data analysis. Structural equation modeling with a robust maximum likelihood method was used to examine the proposed model. To investigate the moderated effects of restaurant type, a latent moderated mediation model was used. Findings: The results showed that consumers' value perceptions toward technology use in restaurants influenced their intention to use ORISST via both hedonic and utilitarian expectations. Latent moderated mediation analyzes revealed that the mediation effect of hedonic expectation between perceived value and the intention was stronger in fine-dining than in quick-service restaurants. Originality/value: This study extends the understanding of consumer intentions to use interactive self-service technology in restaurants by building on a model that is customer-oriented instead of tech-specific. Furthermore, the conditional effects of restaurant type are investigated using the latent moderated structural equation method. The findings of this study provide guidelines for managers of quick-service and fine-dining restaurants to better incorporate ORISST in their restaurants, to boost customer experiences and to increase operational efficiency. [ABSTRACT FROM AUTHOR]

Summary: Lon, a member of the AAA+ protease family, plays vital roles in Type III secretion systems (T3SS), agglutination and colony shape in the model plant pathogen Pseudomonas syringae. Lon also functions as a transcriptional regulator in other bacterial species such as Escherichia coli and Brevibacillus thermoruber. To reveal the molecular mechanisms of Lon as a dual‐function protein in P. syringae, we studied Lon‐regulated genes by using RNA sequencing (RNA‐seq), chromatin immunoprecipitation sequencing (ChIP‐seq) and liquid chromatography–tandem mass spectrometry. As a transcriptional regulator, Lon directly regulated a group of genes (PSPPH_4788, gacA, fur, gntR, clpS, lon and glyA) and consequently regulated their functions, such as 1‐dodecanol oxidation activity, motility, pyoverdine production, glucokinase activity, N‐end rule pathway, lon expression and serine hydroxymethyltransferase activity. Mass spectrometry results revealed that the expression levels of five T3SS proteins (such as HrcV, HrpW1) were higher in the ∆lon strain than the wild‐type (WT) strain in KB. In MM, 12 metabolic proteins (such as AcdS and NuoI) showed lower levels in the ∆lon strain than the WT strain. Taken together, these data demonstrate that the dual‐function protein Lon sophisticatedly regulates virulence and metabolism in P. syringae. [ABSTRACT FROM AUTHOR]

Summary: Pseudomonas syringae is a model phytopathogenic bacterium that uses the type III secretion system (T3SS) to cause lethal diseases in staple crops and thus presents a threat to food security worldwide. Great progress has been made in delineating the biochemical mechanisms and cellular targets of T3SS effectors, but less is known about the signalling pathways and molecular mechanisms of T3SS regulators. In recent years, thanks to the popularity and power of genome‐wide mutant screening and high‐throughput sequencing, new regulatory proteins (such as RhpR, AefR, AlgU and CvsR) and proteases (such as Lon and RhpP) have been identified as T3SS regulators in P. syringae pathovars. The detailed mechanisms of previously illustrated regulators (such as HrpRS, HrpL and HrpGV) have also been further studied. Notably, the two‐component system RhpRS has been determined to play key roles in the modulation of T3SS via direct regulation of hrpRS and other virulence‐related pathways by sensing changes in environmental signals. In addition, secondary messengers (such as c‐di‐GMP and ppGpp) have been shown to fine‐tune the activity of T3SS. Overall, these studies have suggested the existence of a highly intricate regulatory network for T3SS, which controls the pathogenicity of P. syringae. This short review summarizes studies of P. syringae T3SS regulation and the known mechanisms of key regulators. [ABSTRACT FROM AUTHOR]

The applicability of near-infrared (NIR) and mid-infrared (MIR) spectroscopy combined with chemometrics was explored in this study to develop rapid, low-cost and non-destructive spectroscopic methods for classification and quantification of aflatoxins in brown rice. A total of 132 brown rice samples within the aflatoxin concentration range of 0–2435.8 μg/kg were prepared by artificially inoculated with A. flavus and A. parasiticus strains of fungus. For the classification of samples at varying levels of aflatoxin B1, the linear discriminant analysis model obtained correct classification rate of 96.9 and 90.6% for NIR and MIR spectroscopy, respectively. For the simultaneous determination of aflatoxins B1, B2, G1, G2 and the total aflatoxins, partial least squares regression also showed good predictive accuracy for both NIR (rv = 0.936–0.973, RPD = 2.5–4.0) and MIR spectroscopy (rv = 0.922–0.970, RPD = 2.5–4.0). The overall results indicated that the two spectroscopic techniques offered the feasibility to be used as alternative tools for rapid detection of various aflatoxin contaminations in grain. [ABSTRACT FROM AUTHOR]

Two-component systems (TCSs) consist of the biggest group of signal transduction pathways in biology. Although TCSs play key roles in sensing signals to sustain survival and virulence, the genome-wide regulatory variability and conservation and synergistic actions of global TCSs in response to external stimulus are still uncharacterized. Here, we integrate 120 transcriptome sequencing datasets and 38 chromatin immunoprecipitation sequencing datasets of the model phytopathogen Pseudomonas syringae to illustrate how bacterial TCSs dynamically govern their regulatory roles under changing environments. We reveal themes of conservation and variability in bacterial gene regulations in response to changing environments by developing a network-based PSTCSome (Pseudomonas syringae TCS regulome) containing 232 and 297 functional genes under King's B medium and minimal medium conditions, respectively. We identify 7 TCSs regulating the type III secretion system, motility, or exopolysaccharide production. Overall, this study represents an important source to study the plasticity of TCSs among other TCS-containing organisms. [Display omitted] • PSTCSome includes 232 and 297 functional genes in KB and MM conditions, respectively • FimS/AlgR and PSPPH_1906/1907 plastically govern metabolism in KB and MM • PhoBR, CzcSR, ErcS, and Dcsbis contribute to the full activation of T3SS • PhoBR, AlgB/KinB, MerS, and CopRS regulate motility and exopolysaccharide production Xie et al. demonstrate the regulatory plasticity of global P. syringae TCSs in two growth environments by computationally combining the differentially expressed genes of 60 histidine kinases and binding loci of 38 response regulators. The constructed network includes 232 and 297 functional genes in virulence-suppressing and -activating conditions. [ABSTRACT FROM AUTHOR]

Metal concentration in marine sediments is influenced by sedimentation rate. In this study, the metal concentration in sediments of Bohai Bay, China, was adjusted by sedimentation rate, which was derived from the radionuclide dating method. The results showed that the sedimentation rate of Bohai Bay sediments increased from 0.3 to 0.55 g/a over time, especially in the last 30 years since the economic reform in China. The sequence of metal concentrations (mg/kg) is: Cr(97.41) > Zn(73.14) > Cu(20.59) > Pb(16.42) > Cd(0.49). Through the adjustment, the change of metal concentration in sediment cores increased obviously from bottom to surface sediments. It indicated that the increasing sedimentation rate of Bohai Bay in recent years diluted the metal concentration in the sediment. [ABSTRACT FROM AUTHOR]

Eutrophication is a main cause for impairment of freshwater ecosystems, and diffuse phosphorus (P) loss from agricultural land is usually the main cause for freshwater eutrophication. The P index is a simple and practical tool for estimating the potential P loss risk. In a preceding study, a refined P index scheme was developed and validated. In the current study, the relative importance of the 14 input variables used is assessed in order to determine their relative significance to the final P index value. The backpropagation network with Garson's algorithm was employed in order to capture the significance of interactions among the input variables. The study clearly shows the source factors, especially the degree of P saturation (DPS), along with management practices regarding application of inorganic P fertilizer and livestock manure, are the most important factors governing the P loss in the very high and high risk areas. Conversely, the transportation factors governed P loss risk in the low and very low risk areas. Recommended management strategies for mitigation of P loss from the different risk zones are proposed based on the relative importance analysis and practical constraints. A scenario analysis, based on a gradient reduction of DPS, through decreased application of both inorganic P fertilizer and P emissions factors from livestock manure, gave a reduction of average P index from 7.3 to 57 %. Moreover, the proportion of high- and very-high-risk area may be reduced from 38 to 23 % and 24 to 13 %, respectively. [ABSTRACT FROM AUTHOR]

Representative soil samples (n = 60) collected from suburban agricultural land in Tianjin were analyzed to determine 16 PAHs in this study. Accelerated solvent extraction, GPC (Gel Permeation Chromatography), and SPE (Solid Phase Extraction) clean-up procedures were employed for PAH preparation prior to analysis with gas chromatography–mass spectrometry. The concentrations of the total PAHs (T-PAHs) ranged from 228.6 ng/g to 14722.1 ng/g with the mean value of 613.1 ng/g. Bap concentrations in many sites exceeded the suggested standards. Spatial variation of PAHs in soil was illustrated; the pollution status and comparison to other cities were also investigated. Severe PAH soil pollution was observed in some sites near urban areas. Higher PAH concentrations were detected at the downwind side of the urban areas, indicating the influence of human activities. Two indicative ratios (Fl/(Fl+Pyr, Baa/(Baa+Chr)) and principal component analysis were used to identify the possible sources of PAHs. These suggested that coal combustion was still the most important source of PAHs in Tianjin, which coincided well with the previous studies. These data can be further used to assess the health risk associated with soils polluted by PAHs and can help local government find proper ways to reduce PAHs’ pollution in soils. [ABSTRACT FROM AUTHOR]

Water characteristics and prediction of unfrozen water in sweet corn treated with different blanching temperatures (20, 40, 50, 60, 70, 80, 90, and 100 °C/10 min) were investigated by low-field nuclear magnetic resonance (LF-NMR). Transverse relaxation analysis was firstly used to study the changes of water characteristics and distribution. Then, a chemometric method using partial least squares (PLS) method was employed to predict unfrozen water. Four relaxation components were discerned and pertained to vacuolar, cytoplasmic, and extracellular water, and cell wall protons, respectively. The intracellular water in sweet corn was transported to extracellular space after treatment and the loss of intracellular water increased with blanching temperature. Three groups of blanching temperatures were discriminated by principal component analysis. The PLS regression model based on LF-NMR data accurately predicted unfrozen water in blanched sweet corn with an adjusted determination coefficient of 0.97. [ABSTRACT FROM AUTHOR]

The classification analysis and firmness prediction of sweet corn subjected to different treatments were investigated to develop the potential application of low field nuclear magnetic resonance for food quality control. Principal component analysis (PCA) was firstly used for exploiting the invisible changes of the internal characteristics of blanched sweet corn. Then, two classification methods involving regression analysis in combination with linear discriminant analysis (LDA), which is based on data compression technology (PCA and partial least squares, PLS), were compared. The PCA score plots clearly showed that the samples varied according to the temperature of the treatment. For the goal of classification, the principal components extracted from the PLS analysis were more useful than those obtained from PCA. Cross validation was helpful to determine the appropriate number of principal components. In fact, it proved that PLS combined with LDA yielded the highest success classification rate (94.3%), and PLS also performed well in firmness prediction of processed sweet corn. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae, a Gram-negative plant pathogen, expresses multitudinous transcriptional regulators to control the type III secretion system (T3SS) and response to diverse environmental challenges. Although the mechanisms of virulence-associated regulators of P. syringae have been studied for decades, the overall crosstalk underlying these regulators is still elusive. Here, we identify five T3SS regulators (EnvZ-OmpR, CbrAB2, PhoPQ, PilRS, and MgrA), and find that the two-component systems EnvZ-OmpR and CbrAB2 negatively regulate the T3SS. To elucidate crosstalk between 16 virulence-associated regulators in P. syringae , we map an online intricate network called "PSRnet" (Pseudomonas syringae regulatory network) by combining the differentially expressed genes (DEGs) of these 16 regulators by RNA sequencing (RNA-seq) and their binding loci by chromatin immunoprecipitation sequencing (ChIP-seq). Consequently, we identify 238 and 153 functional genes involved in the T3SS and other virulence-related pathways in KB and MM media, respectively. Our results provide insights into the mechanism of plant infections caused by P. syringae. [Display omitted] • EnvZ-OmpR, CbrAB2, PhoPQ, PilRS, and MgrA regulate virulence • A P seudomonas syringae regulatory network (PSRnet) is constructed • PSRnet reveals hundreds of functional genes involved in virulence-related pathways • An online PSRnet platform provides network analysis services for users Shao et al. map an intricate network called "PSRnet" (Pseudomonas syringae regulatory network) by combining the differentially expressed genes (DEGs) of 16 regulators and their binding loci. PSRnet includes hundreds of functional genes involved in the type III secretion system (T3SS) and other virulence-related pathways in different nutrition environments. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae is a Gram-negative and model pathogenic bacterium that causes plant diseases worldwide. Here, we set out to identify binding motifs for all 301 annotated transcription factors (TFs) of P. syringae using HT-SELEX. We successfully identify binding motifs for 100 TFs. We map functional interactions between the TFs and their targets in virulence-associated pathways, and validate many of these interactions and functions using additional methods such as ChIP-seq, electrophoretic mobility shift assay (EMSA), RT-qPCR, and reporter assays. Our work identifies 25 virulence-associated master regulators, 14 of which had not been characterized as TFs before. The authors set out to identify binding motifs for all 301 transcription factors of a plant pathogenic bacterium, Pseudomonas syringae, using HT-SELEX. They successfully identify binding motifs for 100 transcription factors, infer their binding sites on the genome, and validate the predicted interactions and functions. [ABSTRACT FROM AUTHOR]

The virulence of Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is regulated by many transcriptional factors (TFs) that control the expression of quorum sensing and protein secretion systems. Here, we report a genome-wide, network-based approach to dissect the crosstalk between 20 key virulence-related TFs. Using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), as well as RNA-seq, we identify 1200 TF-bound genes and 4775 differentially expressed genes. We experimentally validate 347 of these genes as functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that we call 'Pseudomonas aeruginosa genomic regulatory network' (PAGnet). Analysis of the network led to the identification of novel functions for two TFs (ExsA and GacA) in quorum sensing and nitrogen metabolism. Furthermore, we present an online platform and R package based on PAGnet to facilitate updating and user-customised analyses. The virulence of Pseudomonas aeruginosa is regulated by many transcriptional factors (TFs). Here, the authors study the crosstalk between 20 key virulence-related TFs, validate 347 functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that is available as an online platform. [ABSTRACT FROM AUTHOR]