Correction: Signal transduction pathway mediated by the novel regulator LoiA for low oxygen tension induced Salmonella Typhimurium invasion.

[This corrects the article DOI: 10.1371/journal.ppat.1006429.].

PagR mediates the precise regulation of Salmonella pathogenicity island 2 gene expression in response to magnesium and phosphate signals in Salmonella Typhimurium.

To establish systemic infections, Salmonella enterica serovar Typhimurium (S. Typhimurium) requires Salmonella pathogenicity island 2 (SPI-2) to survive and replicate within macrophages. High expression of many SPI-2 genes during the entire intracellular growth period within macrophages is essential, as it contributes to the formation of Salmonella-containing vacuole and bacterial replication. However, the regulatory mechanisms underlying the sustained induction of SPI-2 within macrophages are not fully understood. Here, we revealed a time-dependent regulation of SPI-2 expression mediated by a novel regulator PagR (STM2345) in response to the low Mg2+ and low phosphate (Pi ) signals, which ensured the high induction of SPI-2 during the entire intramacrophage growth period. Deletion of pagR results in reduced bacterial replication in macrophages and attenuation of systemic virulence in mice. The effects of pagR on virulence are dependent on upregulating the expression of slyA, a regulator of SPI-2. At the early (0-4 hr) and later (after 4 hr) stage post-infection of macrophages, pagR is induced by the low Pi via PhoB/R two-component systems and low Mg2+ via PhoP/Q systems, respectively. Collectively, our findings revealed that the PagR-mediated regulatory mechanism contributes to the precise and sustained activation of SPI-2 genes within macrophages, which is essential for S. Typhimurium systemic virulence.

SoxS is a positive regulator of key pathogenesis genes and promotes intracellular replication and virulence of Salmonella Typhimurium.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important intracellular pathogen, causing gastroenteritis or severe systemic infection in a variety of hosts. During infection, S. Typhimurium must survive and replicate in host macrophages, which produce abundant oxidative compounds. SoxRS regulon is a well-known regulator that is activated in response to oxidative stress and promotes bacterial tolerance to oxidants in E. coli. However, the global regulatory function of SoxS in S. Typhimurium remains poorly characterized. Here, we used an RNA sequencing-based approach to investigate the role of SoxS in the expression of S. Typhimurium virulence genes. Besides the downregulation of genes related to resistance to oxidative stress, we found that in a soxS deletion mutant the expression of Salmonella pathogenicity island (SPI)-2 genes, which are crucial for replication within macrophages, was significantly repressed. Moreover, immunofluorescence and mice infection experiments showed that soxS deletion inhibited replication in macrophages and decreased virulence upon intraperitoneal inoculation in mice, respectively. Collectively, our findings demonstrate that SoxS is a positive regulator of SPI-2 genes and, therefore, plays a crucial role in S. Typhimurium intracellular replication and virulence.

The putative transcriptional regulator STM14_3563 facilitates Salmonella Typhimurium pathogenicity by activating virulence-related genes.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important gram-negative intracellular pathogen that infects humans and animals. More than 50 putative regulatory proteins have been identified in the S. Typhimurium genome, but few have been clearly defined. In this study, the physiological function and regulatory role of STM14_3563, which encodes a ParD family putative transcriptional regulator in S. Typhimurium, were investigated. Macrophage replication assays and mice experiments revealed that S. Typhimurium showed reduced growth in murine macrophages and attenuated virulence in mice owing to deletion of STM14_3563 gene. RNA sequencing (RNA-Seq) data showed that STM14_3563 exerts wide-ranging effects on gene expression in S. Typhimurium. STM14_3563 activates the expression of several genes encoded in Salmonella pathogenicity island (SPI)-6, SPI-12, and SPI-13, which are required for intracellular replication of S. Typhimurium. Additionally, the global transcriptional regulator Fis was found to directly activate STM14_3563 expression by binding to the STM14_3563 promoter. These results indicate that STM14_3563 is involved in the regulation of a variety of virulence-related genes in S. Typhimurium that contribute to its growth in macrophages and virulence in mice.

Structural stability of Co-V intermetallic phases and thermodynamic description of the Co-V system.

The Co-V system has been reviewed. Density functional theory (DFT) calculations using the generalized gradient approximation (GGA) were used to obtain the energies for the end-members for all three intermediate phases, Co3V, σ and CoV3. Results from DFT calculations considering spin polarization were used to evaluate the CALPHAD (Calculation of phase diagrams) model parameters. The method to evaluate the contribution of the magnetism to the energies of Co-rich compounds that was introduced in our previous work is presented in more detail in the present work. For the description of the σ phase, the magnetic part of the total energy is included in the description of the pure Co end-member compound resulting in a non-linear description of the magnetic contribution over composition. The calculated phase diagram obtained from the present CALPHAD description is in good agreement with the experimental data. The metastable FCC-L12 phase diagram was calculated and compared with experimental data.

Signal transduction pathway mediated by the novel regulator LoiA for low oxygen tension induced Salmonella Typhimurium invasion.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major intestinal pathogen of both humans and animals. Salmonella pathogenicity island 1 (SPI-1)-encoded virulence genes are required for S. Typhimurium invasion. While oxygen (O2) limitation is an important signal for SPI-1 induction under host conditions, how the signal is received and integrated to the central SPI-1 regulatory system in S. Typhimurium is not clear. Here, we report a signal transduction pathway that activates SPI-1 expression in response to low O2. A novel regulator encoded within SPI-14 (STM14_1008), named LoiA (low oxygen induced factor A), directly binds to the promoter and activates transcription of hilD, leading to the activation of hilA (the master activator of SPI-1). Deletion of loiA significantly decreased the transcription of hilA, hilD and other representative SPI-1 genes (sipB, spaO, invH, prgH and invF) under low O2 conditions. The response of LoiA to the low O2 signal is mediated by the ArcB/ArcA two-component system. Deletion of either arcA or arcB significantly decreased transcription of loiA under low O2 conditions. We also confirmed that SPI-14 contributes to S. Typhimurium virulence by affecting invasion, and that loiA is the virulence determinant of SPI-14. Mice infection assays showed that S. Typhimurium virulence was severely attenuated by deletion of either the entire SPI-14 region or the single loiA gene after oral infection, while the virulence was not affected by either deletion after intraperitoneal infection. The signal transduction pathway described represents an important mechanism for S. Typhimurium to sense and respond to low O2 conditions of the host intestinal tract for invasion. SPI-14-encoded loiA is an essential element of this pathway that integrates the low O2 signal into the SPI-1 regulatory system. Acquisition of SPI-14 is therefore crucial for the evolution of S. Typhimurium as an intestinal pathogen.

Thermodynamic analysis of the topologically close packed σ phase in the Co-Cr system.

Density functional theory (DFT) calculations show that it is essential to consider the magnetic contribution to the total energy for the end-members of the σ phase. A more straightforward method to use the DFT results in a CALPHAD (Calculation of phase diagrams) description has been applied in the present work. It was found that only the results from DFT calculations considering spin-polarization are necessary to obtain a reliable description of the σ phase. The benefits of this method are: the DFT calculation work can be reduced and the CALPHAD description of the magnetic contribution is more reliable. A revised thermodynamic description of the Co-Cr system is presented which gives improved agreement with experimental phase boundary data for the σ phase.

The LysR-type transcriptional regulator STM0030 contributes to Salmonella Typhimurium growth in macrophages and virulence in mice.

Salmonella enterica serovar Typhimurium (S. Tm) is a major intracellular pathogen that infects humans and animals, and its survival and growth in macrophages is essential for its pathogenicity. More than 50 putative regulatory proteins are encoded by the S. Tm genome, but the functions of these regulatory proteins in mediating S. Tm pathogenicity are largely unknown. In this study, we investigated the biological function of the STM0030 gene, which encodes a putative LysR-type transcriptional regulator. We found that STM0030 is upregulated 2.8-5.7-fold during S. Tm growth in macrophages. Further, mutating this gene decreased bacterial growth in macrophages and attenuated virulence in mice. RNA-sequencing to investigate the regulatory function of STM0030 in S. Tm revealed that 447 genes were differentially expressed between the mutant and the wild-type strains; 429 of these genes were downregulated, suggesting that STM0030 mainly acts as a transcriptional activator. Moreover, the expression of gluconate, maltose, and hexose-p transport genes, as well as allantoin utilization genes were downregulated in the STM0030 mutant; this might be associated with the observed decrease in intracellular replication and pathogenicity of the mutant. Our findings suggest that STM0030 is a new pathogenicity-associated regulatory protein that broadens our understanding of the virulence regulatory network of S. Tm.

YaeB, Expressed in Response to the Acidic pH in Macrophages, Promotes Intracellular Replication and Virulence of Salmonella Typhimurium.

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen that infects humans and animals. Survival and growth in host macrophages represents a crucial step for S. Typhimurium virulence. Many genes that are essential for S. Typhimurium proliferation in macrophages and associated with virulence are highly expressed during the intracellular lifecycle. yaeB, which encodes an RNA methyltransferase, is also upregulated during S. Typhimurium growth in macrophages. However, the involvement of YaeB in S. Typhimurium pathogenicity is still unclear. In this study, we investigated the role of YaeB in S. Typhimurium virulence. Deletion of yaeB significantly impaired S. Typhimurium growth in macrophages and virulence in mice. The effect of yaeB on pathogenicity was related to its activation of pstSCAB, a phosphate (Pi)-specific transport system that is verified here to be important for bacterial replication and virulence. Moreover, qRT-PCR data showed YaeB was induced by the acidic pH inside macrophages, and the acidic pH passed to YeaB through inhibiting global regulator histone-like nucleoid structuring (H-NS) which confirmed in this study can repress the expression of yaeB. Overall, these findings identified a new virulence regulatory network involving yaeB and provided valuable insights to the mechanisms through which acidic pH and low Pi regulate virulence.

Thermodynamic assessment of the Co-Ta system.

The Co-Ta system has been reviewed and the thermodynamic description was re-assessed in the present work. DFT (density functional theory) calculations considering spin polarization were performed to obtain the energies for all end-member configurations of the C14, C15, C36 and µ phases for the evaluation of the Gibbs energies of these phases. The phase diagram calculated with the present description agrees well with the experimental and theoretical data. Considering the DFT results was essential for giving a better description of the µ phase at lower temperatures.

The Effect of Oxygen on Phase Equilibria in the Ti-V System: Impacts on the AM Processing of Ti Alloys.

Oxygen is always a constituent in "real" titanium alloys including titanium alloy powders used for powder-based additive manufacturing (AM). In addition, oxygen uptake during powder handling and printing is hard to control and, hence, it is important to understand and predict how oxygen is affecting the microstructure. Therefore, oxygen is included in the evaluation of the thermodynamic properties of the titanium-vanadium system employing the CALculation of PHAse Diagrams method and a complete model of the O-Ti-V system is presented. The ß-transus temperature is calculated to increase with increasing oxygen content whereas the extension of the α-Ti phase field into the binary is calculated to decrease, which explains the low vanadium solubilities measured in some experimental works. In addition, the critical temperature of the metastable miscibility gap of the ß-phase is calculated to increase to above room temperature when oxygen is added. The effects of oxygen additions on phase fractions, martensite and ω formation temperatures are discussed, along with the impacts these changes may have on AM of titanium alloys.

[Putative regulatory protein STM14_3514 decreases Salmonella Typhimurium invasion of epithelial cells].

Objective: To study the function and mechanism of STM14_3514 gene that encoded in Salmonella pathogenicity island (SPI)-1 of Salmonella enterica serovar Typhimurium strain ATCC 14028. Methods: We constructed STM14_3514 mutant strain and a complemented strain of the mutant. Through mice experiment, attachment assays, invasion assays, macrophage replication assays, western blot, and Quantitative real-time PCR analysis (qRT-PCR), we compared the virulence of the mutant strain to that of the wild-type 14028. Results: STM14_3514 mutant shows increased virulence to mice, and the bacterial number of STM14_3514 mutant in liver, spleen, and ileum was more abundant than that of the wild-type strain. The increased virulence of STM14_3514 mutant is caused by its elevated invasion ability to epithelial cells (>2-fold and P<0.05). qRT-PCR and western blot results show that STM14_3514 reduced the expression of HilA and another SPI-1invasion locus. Moreover, the repression of HilA by STM14_3514 is mediated by HilC. Conclusion: STM14_3514 is a negative regulator in SPI-1, which can repress HilA and SPI-1invasion locus through HilC, and possibly contribute to the repression on SPI-1 after bacterial invasion.

Pre-drying limitedly affected the yield, fuel properties, pyrolysis and combusion behavior of sewage sludge hydrochar.

While pre-drying of sewage sludge prior to hydrothermal carbonization is rarely practiced, various pre-drying methods have been performed in literature at lab-scale for convenient solid-to-liquid ratio adjustment. This has created a barrier for comparing hydrochar quality between different studies. Given pre-drying can destroy the floc structure of sewage sludge, we hypothesize that pre-drying may promote the hydrolysis step during hydrothermal carbonization process, resulting in improved hydrochar quality with low nitrogen content. In the current study, the influence of different pre-drying methods (freeze-dry, air-dry and vacuum-dry at 70 °C and 105 °C) on the subsequent hydrothermal carbonization of sewage sludge at 220 °C was assessed in terms of sewage sludge and hydrochar's chemical composition, fuel properties, pyrolysis and combustion behavior, as well as the characterization of the liquid phase. The results indicate that although pre-drying impacts sewage sludge's chemical composition, pyrolysis and combustion behavior, no significant differences exist in the yield, chemical composition, fuel properties, and pyrolysis and combustion behavior of the hydrochar. Therefore, the use of pre-drying would not affect the hydrothermal carbonization process of sewage sludge, and a comparison can be made on hydrochar quality between different studies with or without pre-drying.

Fucoidan derived from Undaria pinnatifida induces apoptosis in human hepatocellular carcinoma SMMC-7721 cells via the ROS-mediated mitochondrial pathway.

Fucoidans, fucose-enriched sulfated polysaccharides isolated from brown algae and marine invertebrates, have been shown to exert anticancer activity in several types of human cancer, including leukemia and breast cancer and in lung adenocarcinoma cells. In the present study, the anticancer activity of the fucoidan extracted from the brown seaweed Undaria pinnatifida was investigated in human hepatocellular carcinoma SMMC-7721 cells, and the underlying mechanisms of action were investigated. SMMC-7721 cells exposed to fucoidan displayed growth inhibition and several typical features of apoptotic cells, such as chromatin condensation and marginalization, a decrease in the number of mitochondria, and in mitochondrial swelling and vacuolation. Fucoidan-induced cell death was associated with depletion of reduced glutathione (GSH), accumulation of high intracellular levels of reactive oxygen species (ROS), and accompanied by damage to the mitochondrial ultrastructure, depolarization of the mitochondrial membrane potential (MMP, Δψm) and caspase activation. Moreover, fucoidan led to altered expression of factors related to apoptosis, including downregulating Livin and XIAP mRNA, which are members of the inhibitor of apoptotic protein (IAP) family, and increased the Bax-to-Bcl-2 ratio. These findings suggest that fucoidan isolated from U. pinnatifida induced apoptosis in SMMC-7721 cells via the ROS-mediated mitochondrial pathway.

ClusterNet: a clustering distributed prior embedded detection network for early-stage esophageal squamous cell carcinoma diagnosis.

BACKGROUND: Early and accurate diagnosis of esophageal squamous cell carcinoma (ESCC) is important for reducing mortality. Analyzing intrapapillary capillary loops' (IPCLs) patterns on magnification endoscopy with narrow band imaging (ME-NBI) has been demonstrated effective in the diagnosis of early-stage ESCC. However, even experienced endoscopists may face difficulty in finding and classifying countless IPCLs on ME-NBI. PURPOSE: We propose a novel clustering prior embedded detection network: ClusterNet. ClusterNet is capable of analyzing the distribution of IPCLs on ME-NBI automatically and enables endoscopists to overview multiple types of visualization. With ClusterNet assisting, endoscopists may observe ME-NBI images more efficiently, thus they may also predict the pathology and make medical decisions more easily. METHODS: We propose the first large-scale ME-NBI dataset with fine-grained annotations by consensus of expert endoscopists. The dataset is splitted into a training set and an independent testing set based on patients. With two strategies for embedding, ClusterNet can automatically take the clustering effect into consideration. Prior to this work, none of the existing approaches take the clustering effect, which is rather important in classifying the IPCLs, into account. RESULTS: ClusterNet achieves an average precision of 81.2% and an average recall of 90.0% for the detection of IPCLs patterns on each patient of the independent testing set. We also compare ClusterNet with other state-of-the-art detection approaches. The performance of ClusterNet with embedding strategies is consistently superior to that of other approaches in terms of average precision, recall and F2-Score. CONCLUSIONS: Experiments demonstrate that our proposed method is able to detect almost all the IPCLs patterns on ME-NBI and classify them according to the Japanese Endoscopic Society (JES) classification accurately.

Salmonella Typhimurium reprograms macrophage metabolism via T3SS effector SopE2 to promote intracellular replication and virulence.

Salmonella Typhimurium establishes systemic infection by replicating in host macrophages. Here we show that macrophages infected with S. Typhimurium exhibit upregulated glycolysis and decreased serine synthesis, leading to accumulation of glycolytic intermediates. The effects on serine synthesis are mediated by bacterial protein SopE2, a type III secretion system (T3SS) effector encoded in pathogenicity island SPI-1. The changes in host metabolism promote intracellular replication of S. Typhimurium via two mechanisms: decreased glucose levels lead to upregulated bacterial uptake of 2- and 3-phosphoglycerate and phosphoenolpyruvate (carbon sources), while increased pyruvate and lactate levels induce upregulation of another pathogenicity island, SPI-2, known to encode virulence factors. Pharmacological or genetic inhibition of host glycolysis, activation of host serine synthesis, or deletion of either the bacterial transport or signal sensor systems for those host glycolytic intermediates impairs S. Typhimurium replication or virulence.

Protective role of citric acid against oxidative stress induced by heavy metals in Caenorhabditis elegans.

The adverse effects of heavy metals, such as cadmium, zinc, and copper, occur due to the generation of reactive oxygen species (ROS). The use of Caenorhabditis elegans for the purposes of conservation and biomonitoring is of great interest. In the present study, ROS, malondialdehyde (MDA), and citric acid levels and superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities in a model organism were tested to study toxicity. C. elegans was exposed to three different concentrations of cadmium (CdCl2, 5, 10, 50 µM), zinc (ZnSO4, 10, 100, 500 µM), and copper (CuSO4, 10, 100, 500 µM) for 3 days. ROS levels increased by 1.3- to 2.1-fold with increasing metal concentrations. The MDA content increased by approximately 7-, 5-, 2-fold after exposure to high concentrations of cadmium, zinc, and copper, respectively. Furthermore, the citric acid content increased by approximately 3-fold in the cadmium (Cd, 5 µM), zinc (Zn, 10 µM), and copper (Cu, 100 µM) treatment groups compared to that in untreated C. elegans. Therefore, citric acid may play an important role in heavy metal detoxification. Excess citric acid also slightly increased the LC50 by 1.3- to 2.0-fold, basic movements by 1.0- to 1.5-fold, decreased the ROS content by 2.4- to 2.1-fold, the MDA content by 4- to 2-fold, the SOD activity by 9- to 3-fold, the GPx activity by 4.0- to 3.0-fold, and the mRNA expression levels of GPxs by 3.2- to 1.8-fold after metals treatment. And it is most significantly in the alleviation of citric acid to cadmium. This study not only provides information to further understand the effects of heavy metal exposure on ROS, MDA, GPx, SOD, and citric acid in worms but also indicates that supplemental citric acid can protect animals from heavy metal stress and has broad application prospects in decreasing oxidative damage caused by heavy metals.

RstA, a two-component response regulator, plays important roles in multiple virulence-associated processes in enterohemorrhagic Escherichia coli O157:H7.

BACKGROUND: Enterohemorrhagic Escherichia coli O157:H7 (EHEC O157) causes bloody diarrhea and hemolytic-uremic syndrome. EHEC O157 encounters varied microenvironments during infection, and can efficiently adapt to these using the two-component system (TCS). Recently, a functional TCS, RstAB, has been implicated in the regulation of virulence of several bacterial pathogens. However, the regulatory function of RstAB in EHEC O157 is poorly understood. This study aimed at providing insights into the global effects of RstA on gene expression in EHEC O157. RESULTS: In the present study, we analyzed gene expression differences between the EHEC O157 wild-type strain and a ΔrstA mutant using RNA-seq technology. Genes with differential expression in the ΔrstA mutant compared to that in the wild-type strain were identified and grouped into clusters of orthologous categories. RstA promoted EHEC O157 LEE gene expression, adhesion in vitro, and colonization in vivo by indirect regulation. We also found that RstA could bind directly to the promoter region of hdeA and yeaI to enhance acid tolerance and decrease biofilm formation by modulating the concentration of c-di-GMP. CONCLUSIONS: In summary, the RstAB TCS in EHEC O157 plays a major role in the regulation of virulence, acid tolerance, and biofilm formation. We clarified the regulatory function of RstA, providing an insight into mechanisms that may be potential drug targets for treatment of EHEC O157-related infections.

Evaluation of sulfuryl fluoride as a soil fumigant in China.

BACKGROUND: Root-knot nematodes and soil-borne diseases constrain the rapid development of protected agriculture in China, especially while phasing out methyl bromide (MB). The fumigant sulfuryl fluoride (SF) is currently used as an alternative to MB for the disinfestation of buildings and post-harvest commodities. Our experiments aimed to evaluate a novel application of SF as a soil fumigant in greenhouses in China. RESULTS: Dose-response experiments indicated that SF has good efficacy on root-knot nematodes (Meloidogyne spp.) and moderate activity against Fusarium spp. and weeds (Digitaria sanguinalis (L.) Scop. and Abutilon theophrasti Medicus). The field trials indicates that SF has good efficacy, between 80 and 94%, on Meloidogyne spp., and Fusarium spp. at the rates of 25-50 g m(-2) in tomato and cucumber in Beijing and Shandong Province. Marketable yield and plant vigour was not significantly different in SF and MB treatments. SF has lower emissions than MB during the fumigation operation. It is simple to apply, can be used at low temperature, and has a short plant-back time. SF was found to be an economically feasible alternative to MB for nematode control in China. CONCLUSION: SF can be used as a soil fumigant to control root-knot nematodes and to reduce the levels of key soil pathogens.

Anti-metastasis effect of fucoidan from Undaria pinnatifida sporophylls in mouse hepatocarcinoma Hca-F cells.

Metastasis is one of the major causes of cancer-related death. It is a complex biological process involving multiple genes, steps, and phases. It is also closely connected to many biological activities of cancer cells, such as growth, invasion, adhesion, hematogenous metastasis, and lymphatic metastasis. Fucoidan derived from Undaria pinnatifida sporophylls (Ups-fucoidan) is a sulfated polysaccharide with more biological activities than other fucoidans. However, there is no information on the effects of Ups-fucoidan on tumor invasion and metastasis. We used the mouse hepatocarcinoma Hca-F cell line, which has high invasive and lymphatic metastasis potential in vitro and in vivo, to examine the effect of Ups-fucoidan on cancer cell invasion and metastasis. Ups-fucoidan exerted a concentration- and time-dependent inhibitory effect on tumor metastasis in vivo and inhibited Hca-F cell growth, migration, invasion, and adhesion capabilities in vitro. Ups-fucoidan inhibited growth and metastasis by downregulating vascular endothelial growth factor (VEGF) C/VEGF receptor 3, hepatocyte growth factor/c-MET, cyclin D1, cyclin-dependent kinase 4, phosphorylated (p) phosphoinositide 3-kinase, p-Akt, p-extracellular signal regulated kinase (ERK) 1/2, and nuclear transcription factor-κB (NF-κB), and suppressed adhesion and invasion by downregulating L-Selectin, and upregulating protein levels of tissue inhibitor of metalloproteinases (TIMPs). The results suggest that Ups-fucoidan suppresses Hca-F cell growth, adhesion, invasion, and metastasis capabilities and that these functions are mediated through the mechanism involving inactivation of the NF-κB pathway mediated by PI3K/Akt and ERK signaling pathways.