FURION: modeling of FEL pulses propagation in dispersive soft X-ray beamline systems.

Modern X-ray free-electron lasers (XFELs) can generate pulses with durations ranging from femtoseconds to attoseconds. The numerical evaluation of ultra-short XFEL pulses through beamline systems is a critical process of beamline system design. However, the bandwidth of such ultra-short XFEL pulses is often non-negligible, and the propagation cannot be simply approximated using the central wavelength, especially in dispersive beamline systems. We developed a numerical model which is called Fourier optics based Ultrashort x-Ray pulse propagatION tool (FURION). This model can not only be used to simulate dispersive beamline systems but also to evaluate non-dispersive beamline systems. The FURION model utilizes Fresnel integral and angular spectrum integral to perform ultra-short XFEL pulse propagation in free space. We also present the method for XFEL pulse propagation through different types of dispersive gratings, which are commonly used in soft X-ray beamline systems. By using FURION, a start-to-end simulation of the FEL-1 beamline system at Shenzhen superconducting soft X-ray free electron laser (S3FEL) is carried out. This model can also be used to evaluate gratings-based spectrometers, beam splitters, pulse compressors, and pulse stretchers. This work provides valuable insights into the start-to-end simulation of X-ray beamline systems.

Spatiotemporal response of concave VLS grating to ultra-short X-ray pulses.

In soft X-ray free-electron laser (FEL) beamlines, variable-line-spacing (VLS) gratings are often used as dispersive components of monochromators and spectrometers due to their combined dispersion and focusing properties. X-ray FEL pulses passing through the VLS grating can result in not only transverse focusing but also spatiotemporal coupling effects, such as pulse front tilt, pulse front rotation, and pulse stretching. In this paper, we present a theoretical study of the spatiotemporal response of concave VLS gratings to ultra-short X-ray pulses. The theoretical analysis indicates that the tilt angle of the non-zero diffraction orders varies with the propagation distance, and disappears at the focus, where the focal lengths and pulse stretching differ for different diffraction orders. The model demonstrates the pulse duration after the concave VLS grating is the convolution of the initial pulse duration and the stretching term induced by dispersion, while the beam size at the focus in x dimension is the convolution of the geometric scaling beam size and the dispersion term. This work provides a mathematical explanation for the spatiotemporal response of concave VLS grating to ultra-short X-ray pulses and offers valuable insights into the design of FEL grating monochromators, spectrometers, pulse compressors, and pulse stretchers.

Stereoselective and Divergent Aza-Adenosine and Aza-Guanosine Syntheses from Xylofuranose, the Key Fragments of a STING Cyclic Dinucleotide Agonist.

The stereoselective and divergent synthesis of two aza-nucleosides is reported. Starting from xylofuranose 9, aza-adenosine 2 was prepared in 13 steps and 7% overall yield, and aza-guanosine 3 was prepared in 13 steps and 7.8% overall yield. Compared to the original syntheses, some advantages of these new routes are significant yield improvement, overall step-count reduction, an optimized protecting group strategy, the development of a versatile platform for nitrogenous base incorporation, and the elimination of hazardous reagents (e.g., benzyl isocyanate, Et3N·HF).

Characterization of pathogenic roles of two Erysipelothrix rhusiopathiae surface proteins.

Erysipelothrix rhusiopathiae is the causative agent of animal erysipelas and human erysipeloid. E. rhusiopathiae HP0728 and HP1472 have been reported to be down regulated in low-virulence or avirulent strains, but their pathogenic roles are not known. In this study, it was found that E. rhusiopathiae HP0728 and HP1472 were displayed on the surface of E. rhusiopathiae. Moreover, recombinant HP1472 could adhere to pig vascular endothelial cells. Recombinant HP0728 could bind host plasminogen but could not bind fibronectin. In conclusion, our work suggested that HP0728 and HP1472 are virulence factors of E. rhusiopathiae.

Glyceraldehyde-3-phosphate dehydrogenase acts as an adhesin in Erysipelothrix rhusiopathiae adhesion to porcine endothelial cells and as a receptor in recruitment of host fibronectin and plasminogen.

Erysipelothrix rhusiopathiae is the causative agent of animal erysipelas and human erysipeloid. Previous studies suggested glyceraldehyde 3-phosphate dehydrogenase (GAPDH) plays a role in the pathogenesis of E. rhusiopathiae infection. We studied E. rhusiopathiae GAPDH interactions with pig vascular endothelial cells, fibronectin, and plasminogen. Recombinant GAPDH (rGAPDH) was successfully obtained, and it was shown that it plays a role in E. rhusiopathiae adhesion to pig vascular endothelial cells. Moreover, rGAPDH could bind fibronectin and plasminogen in a dose-dependent manner. To our knowledge, this is the first study demonstrating that a moonlighting protein plays a role in pathogenesis of E. rhusiopathiae infections.

Synthesis of HIV-Maturation Inhibitor BMS-955176 from Betulin by an Enabling Oxidation Strategy.

A concise and scalable second generation synthesis of HIV maturation inhibitor BMS-955176 is described. The synthesis is framed by an oxidation strategy highlighted by a CuI mediated aerobic oxidation of betulin, a highly selective PIFA mediated dehydrogenation of an oxime, and a subsequent Lossen rearrangement which occurs through a unique reaction mechanism for the installation of the C17 amino functionality. The synthetic route proceeds in 7 steps with 47% overall yield and begins from the abundant and inexpensive natural product betulin.

Exogenous application of silicon and selenium improves the tolerance of tomato plants to calcium nitrate stress.

Silicon (Si) and selenium (Se) can improve the tolerance of plants to NaCl-induced salt stress. However, few studies are available on their regulatory effects on plants' tolerance to calcium nitrate stress, which often occurs in protected facilities, causing secondary soil salinization. In this study, we report the effects of Si (6 mM) and Se (20 µM) applied separately or in combination on the growth, photosynthesis, oxidative damage, and nitrogen metabolism of tomato plants, as well as fruit quality under calcium nitrate stress. The results showed that applications of Si or Se alone or in combination improved the plant growth and photosynthetic performance and reduced oxidative damage of the stressed plants. Applications of Si and Se did not decrease the calcium accumulation in leaves of the stressed plants. Under calcium nitrate stress, the concentrations of NO3-, NO2- and NH4+ in leaves were significantly increased, while the activities of nitrogen assimilation-related enzymes (including nitrate reductase, nitrite reductase, glutamine synthase, glutamine-2-oxoglutarate aminotransferase and glutamate dehydrogenase) were decreased. Applications of Si and Se, especially their combined treatment, decreased the NO3-, NO2-, and NH4+ concentrations and enhanced the activities of nitrogen assimilation-related enzymes in the stressed plants. Applied Si and Se also decreased the nitrate and titratable acid concentrations and increased vitamin levels in tomato fruits under calcium nitrate stress. It is suggested that Si and Se improved the tomato plant growth and fruit quality under calcium nitrate stress by alleviating oxidative damage and promoting both photosynthesis and nitrogen assimilation.

Shape optimization design of the offset mirror in FEL-1 beamline at S3FEL.

Nowadays, due to the advantages of high peak power, high average power, ultra-short pulse, and fully coherent characteristics, the high-repetition-rate free-electron laser (FEL) is thriving in many countries around the world. The thermal load caused by high-repetition-rate FEL poses a great challenge to the mirror surface shape. Especially in the case of high average power, how to perfectly control the mirror shape to maintain the coherence of the beam has become a difficult problem in beamline design. In addition to multi-segment PZT, when multiple resistive heaters are used to compensate for the mirror shape, the heat flux (or power) generated by each heater must be optimized to obtain sub-nanometer height error. This article establishes MHCKF model for the mirror surface deformation under the combined effect of the mirror initial deformation, the thermal deformation caused by X-rays, and the deformation compensated by multiple heaters. By searching the perturbation term in the mathematical model, the least squares solution of the heat fluxes generated by all heaters can be obtained. This method can not only set multiple constraints on the heat fluxes but also quickly obtain their values when minimizing the mirror shape error. It overcomes the problem of time-consuming optimization processes encountered by traditional finite element analysis software, especially in the context of multi-parameter optimization. This article focuses on the offset mirror in the FEL-1 beamline at S3FEL. Using this method, the optimization of 25 heat fluxes generated by all resistive heaters was accomplished within a few seconds utilizing an ordinary laptop. The results indicate that the height error RMS decreased from 40 nm to 0.009 nm, and the slope error RMS reduced from 192.7nrad to 0.4nrad. Wave-optics simulations show that the wavefront quality has been significantly improved. In addition, some factors affecting mirror shape error, such as the number of heaters, higher repetition rate, film coefficient, and the length of copper tube, were analyzed. The results show that the MHCKF model and optimization algorithm can effectively solve the optimization problem of compensating for the mirror shape with multiple heaters.

An optimized side-cooling scheme for a collimation mirror at the SSRF.

Here, in order to reduce tangential slope errors along the centreline of a first mirror's surface, a side-cooling scheme is proposed. The length of the contact area between the mirror and cooling blocks should be smaller than the beam footprint along the mirror. By optimizing the length and the height of the contact area, reduced slope errors can be obtained. Using this scheme the maximum temperature is not located at the centre of the footprint but shifts to both sides, which fundamentally changes the temperature distribution and enhances the cooling effect compared with the traditional method. This paper presents a `design of experiment' analysis for four kinds of cooling schemes. The structure of the mechanical clamps is also described.

Integrated metabolome and transcriptome analysis reveals salicylic acid and flavonoid pathways' key roles in cabbage's defense responses to Xanthomonas campestris pv. campestris.

Xanthomonas campestris pv. campestris (Xcc) is a vascular bacteria pathogen causing black rot in cabbage. Here, the resistance mechanisms of cabbage against Xcc infection were explored by integrated metabolome and transcriptome analysis. Pathogen perception, hormone metabolisms, sugar metabolisms, and phenylpropanoid metabolisms in cabbage were systemically re-programmed at both transcriptional and metabolic levels after Xcc infection. Notably, the salicylic acid (SA) metabolism pathway was highly enriched in resistant lines following Xcc infection, indicating that the SA metabolism pathway may positively regulate the resistance of Xcc. Moreover, we also validated our hypothesis by showing that the flavonoid pathway metabolites chlorogenic acid and caffeic acid could effectively inhibit the growth of Xcc. These findings provide valuable insights and resource datasets for further exploring Xcc-cabbage interactions and help uncover molecular breeding targets for black rot-resistant varieties in cabbage.

Large-scale identification of bacteria-host crosstalk by affinity chromatography: capturing the interactions of Streptococcus suis proteins with host cells.

Protein-protein interactions between bacteria and their hosts are responsible for all types of infection processes. The investigation of the bacteria-host crosstalk can provide a comprehensive understanding of the pathogenesis of bacterial disease. Despite scattered efforts in this field, a systematic identification of interactions between host and bacterial proteins remains unavailable. Here, we develop ACSP (affinity chromatography-based surface proteomics), which combines affinity chromatography and shotgun proteomics (LC-MS/MS), to investigate the interactions on a large-scale. Using ACSP, the potential surface interacting proteins (SIPs) of Streptococcus suis serotype 2 (SS2) were captured by the chromatographic resin, which was immobilized with the native surface molecules of Hep-2 cells. And then 40 potential SIPs were identified from the preys by LC-MS/MS, including 3 SIPs that have been previously reported in the literature. We selected 8 important SIPs and confirmed their ability to adhere to Hep-2 cells. Additionally, 3 newly identified SIPs, or their polyclonal antibodies, were found to significantly inhibit the adherence of SS2 to Hep-2 cells, indicating their essential role in the interaction between SS2 and Hep-2 cells. Using this example, we show that ACSP represents a new valuable tool for investigating the bacteria-host interactions.

Comparative Transcriptomic Analysis of Gene Expression Inheritance Patterns Associated with Cabbage Head Heterosis.

The molecular mechanism of heterosis or hybrid vigor, where F1 hybrids of genetically diverse parents show superior traits compared to their parents, is not well understood. Here, we studied the molecular regulation of heterosis in four F1 cabbage hybrids that showed heterosis for several horticultural traits, including head size and weight. To examine the molecular mechanisms, we performed a global transcriptome profiling in the hybrids and their parents by RNA sequencing. The proportion of genetic variations detected as single nucleotide polymorphisms and small insertion-deletions as well as the numbers of differentially expressed genes indicated a larger role of the female parent than the male parent in the genetic divergence of the hybrids. More than 86% of hybrid gene expressions were non-additive. More than 81% of the genes showing divergent expressions showed dominant inheritance, and more than 56% of these exhibited maternal expression dominance. Gene expression regulation by cis-regulatory mechanisms appears to mediate most of the gene expression divergence in the hybrids; however, trans-regulatory factors appear to have a higher effect compared to cis-regulatory factors on parental expression divergence. These observations bring new insights into the molecular mechanisms of heterosis during the cabbage head development.

HP0487 contributes to the virulence of Streptococcus suis serotype 2 by mediating bacterial adhesion and anti-phagocytosis to neutrophils.

Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen that poses a serious threat to human health and the swine industry. The survival and travel in the bloodstream are the important causes for SS2, contributing to bacteremia, septicemia even septic shock. However, the related mechanism remains largely unknown. Preliminary experiment demonstrated that SS2 could largely attach to the surface of neutrophils, implying that this phenomenon maybe contributed to the travel of SS2 in bloodstream and then influenced its pathogenicity. To confirm this hypothesis, using a previously established screening method that combines affinity chromatography (based on liquid chromatography-tandem mass spectrometry) with shotgun proteomics, three candidate proteins (HP0487, HP1765, and HP1111) were identified from SS2 that could interact with neutrophils. Next, by constructing the deletion mutations, we demonstrated that HP0487 of three proteins could significantly influence the adhesion of SS2 to neutrophils. Furthermore, HP0487 was shown to contribute to the anti-phagocytosis of SS2 to neutrophils and RAW264.7 cells. More importantly, the deletion of HP0487 significantly reduced lethality and bacterial loads in vivo of SS2. Thus, our findings demonstrate that HP0487 contributes to SS2 virulence by mediating the adhesion and anti-phagocytosis of SS2 to neutrophils, promoting a better understanding about the pathogenesis of SS2.

Screening of Virulence-Related Transcriptional Regulators in Streptococcus suis.

Streptococcus suis (S.suis) is an important zoonotic pathogen that causes many severe diseases in pigs and humans. Virulence-related transcriptional regulators have been widely reported in pathogenic microorganisms, but only a few have been identified in S.suis. Our aim was to screen virulence-related transcriptional regulators in S.suis. A total of 89 such genes were predicted in the S.suis genome, of which 22 were up-regulated and 18 were down-regulated during S.suis infection in mice. To evaluate the roles of these differentially expressed factors in S.suis virulence, deletion mutants were constructed, and 10 mutants were successfully obtained. Among these genes, the deletion of comR, sitR, or sxvR caused significantly decreased virulence in mice, compared to that with the wild-type strain. Moreover, the survival of ΔcomR, ΔsitR, and ΔsxvR mutant strains in blood was significantly reduced both in vitro and in vivo. Furthermore, their pro-inflammatory abilities were also obviously decreased in vivo. The regulatory mechanisms of comR, sitR, and sxvR were then analyzed by whole transcriptome RNA sequencing (RNA-Seq). Results indicated that the absence of comR induced the down-regulation of 17 virulence factors or virulence-related factors, including genes involved in the synthesis of capsules, oxidative stress tolerance, immune evasion, and cell division. Furthermore, three and two virulence factors or virulence-related factors were down-regulated upon deletion of sitR and sxvR, respectively. Thus, this study reports the discovery of three virulence-associated transcriptional regulatory factors in S.suis. These factors could ultimately be targeted to control infection caused by these bacteria.

Process research and development for a tetrazole-based growth hormone secretagogue (GHS) pharmaceutical development candidate.

BMS-317180 (1) is a potent, orally active agonist of the human growth hormone secretagogue (GHS) receptor. This manuscript details the process research and development efforts that enabled the synthesis of the phosphate salt of 1 on a multi-kilogram scale. Key considerations in the development of this process focused on safe execution and the requirement for telescoped synthetic transformations (i.e., without isolation of intermediate products) to contend with a lack of suitably crystalline products.

HP1717 Contributes to Streptococcus suis Virulence by Inducing an Excessive Inflammatory Response and Influencing the Biosynthesis of the Capsule.

Streptococcus suis 2 (SS2) is an important zoonotic pathogen that substantially harms the swine industry and poses threats to human health. Excessive inflammation is considered to be a hallmark of SS2 infection because it is responsible for most clinical signs of SS2, especially streptococcal toxic shock-like syndrome. However, the current knowledge of SS2-induced excessive inflammation remains limited. In this study, we identified HP1717 as a novel extracellular pro-inflammatory protein in SS2 that can induce robust expression of inflammatory cytokines in RAW264.7 macrophages. Notably, the pro-inflammatory ability of HP1717 was dose-dependent and heat-sensitive, and it required the recognition of Toll-like receptor 2 (TLR2) and the phosphorylation of both extracellular signal-regulated kinases 1/2 (ERK1/2) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Further, by constructing a deletion mutant, we demonstrated that HP1717 significantly influenced the biosynthesis of the bacterial capsule, which plays a critical role in the virulence of SS2 by interfering with the ability of host immune cells to phagocytize and kill the pathogen. Indeed, the mutant strain displayed reduced resistance to whole-blood killing compared with the wild strain. Finally, murine experiments indicated that the deletion of hp1717 in SS2 reduced the lethality, pro-inflammatory activity, and bacterial loads in mice. Collectively, our data reveal HP1717 as a novel virulence-related factor of SS2 that can induce an excessive inflammatory response and significantly affect the bacterial capsule, thus expanding our understanding of the pathogenesis of S. suis.

Streptococcus suis 2 Transcriptional Regulator TstS Stimulates Cytokine Production and Bacteremia to Promote Streptococcal Toxic Shock-Like Syndrome.

Two large-scale outbreaks of streptococcal toxic shock-like syndrome (STSLS) have revealed Streptococcus suis 2 to be a severe and evolving human pathogen. We investigated the mechanism by which S. suis 2 causes STSLS. The transcript abundance of the transcriptional regulator gene tstS was found to be upregulated during experimental infection. Compared with the wild-type 05ZY strain, a tstS deletion mutant (ΔtstS) elicited reduced cytokine secretion in macrophages. In a murine infection model, tstS deletion resulted in decreased virulence and bacterial load, and affected cytokine production. Moreover, TstS expression in the P1/7 strain of S. suis led to the induction of STSLS in the infected mice. This is noteworthy because, although it is virulent, the P1/7 strain does not normally induce STSLS. Through a microarray-based comparative transcriptomics analysis, we found that TstS regulates multiple metabolism-related genes and several virulence-related genes associated with immune evasion.

Direct Growth of Graphene on Silicon by Metal-Free Chemical Vapor Deposition.

The metal-free synthesis of graphene on single-crystal silicon substrates, the most common commercial semiconductor, is of paramount significance for many technological applications. In this work, we report the growth of graphene directly on an upside-down placed, single-crystal silicon substrate using metal-free, ambient-pressure chemical vapor deposition. By controlling the growth temperature, in-plane propagation, edge-propagation, and core-propagation, the process of graphene growth on silicon can be identified. This process produces atomically flat monolayer or bilayer graphene domains, concave bilayer graphene domains, and bulging few-layer graphene domains. This work would be a significant step toward the synthesis of large-area and layer-controlled, high-quality graphene on single-crystal silicon substrates.

HP1330 Contributes to Streptococcus suis Virulence by Inducing Toll-Like Receptor 2- and ERK1/2-Dependent Pro-inflammatory Responses and Influencing In Vivo S. suis Loads.

Streptococcus suis 2 (SS2) has evolved into a highly invasive pathogen responsible for two large-scale outbreaks of streptococcal toxic shock-like syndrome (STSLS) in China. Excessive inflammation stimulated by SS2 is considered a hallmark of STSLS, even it also plays important roles in other clinical symptoms of SS2-related disease, including meningitis, septicemia, and sudden death. However, the mechanism of SS2-caused excessive inflammation remains poorly understood. Here, a novel pro-inflammatory protein was identified (HP1330), which could induce robust expression of pro-inflammatory cytokines (TNF-α, MCP-1, and IL-1ß) in RAW264.7 macrophages. To evaluate the role of HP1330 in SS2 virulence, an hp1330-deletion mutant (Δhp1330) was constructed. In vitro, hp1330 disruption led to a decreased pro-inflammatory ability of SS2 in RAW 264.7 macrophages. In vivo, Δhp1330 showed reduced lethality, pro-inflammatory activity, and bacterial loads in mice. To further elucidate the mechanism of HP1330-induced pro-inflammatory cytokine production, antibody blocking and gene-deletion experiments with macrophages were performed. The results revealed that the pro-inflammatory activity of HP1330 depended on the recognition of toll-like receptor 2 (TLR2). Furthermore, a specific inhibitor of the extracellular signal-regulated kinase 1/2 (ERK1/2) pathways could significantly decrease HP1330-induced pro-inflammatory cytokine production, and western blot analysis showed that HP1330 could induce activation of the ERK1/2 pathway. Taken together, our findings demonstrate that HP1330 contributes to SS2 virulence by inducing TLR2- and ERK1/2-dependent pro-inflammatory cytokine production and influencing in vivo bacterial loads, implying that HP1330 may be associated with STSLS caused by SS2.

iTRAQ-based quantitative proteomic analysis reveals potential virulence factors of Erysipelothrix rhusiopathiae.

Erysipelothrix rhusiopathiae is a ubiquitous pathogen that has caused considerable economic losses to pig farmers. However, the mechanisms of E. rhusiopathiae pathogenesis remain unclear. To identify new virulence-associated factors, the differentially abundant cell wall-associated proteins (CWPs) between high- and low-virulence strains were investigated through isobaric Tags for Relative and Absolute Quantitation (iTRAQ) combined with liquid chromatography-quadrupole mass spectrometry (LC-MS/MS). In total, 100 CWPs showed significant differences in abundance. Selected differences were verified by western blotting to support the iTRAQ data. Among the differential proteins, the proteins with higher abundance in the high-virulence strain were mostly ABC transporter proteins and adhesion proteins, and the proteins with lower abundance in the high-virulence strain were mainly stress-response proteins. The more abundant proteins in the high-virulence strain may be related to bacterial virulence. The iTRAQ results showed that the abundance of the sugar ABC transporter substrate-binding protein Sbp (No. 5) was higher by 1.73-fold. We further constructed an sbp-deletion mutant. Experiments in animal models showed that the sbp-deletion mutant caused decreased mortality. Together, our data indicated that transporter proteins and adhesion proteins may play important roles in E. rhusiopathiae virulence and confirmed that sbp contributed to the virulence of E. rhusiopathiae. BIOLOGICAL SIGNIFICANCE: To our knowledge, this is the first proteomic analysis comparing differentially abundant CWPs between high- and low-virulence E. rhusiopathiae strains by iTRAQ. We generated comprehensive and accurate lists of E. rhusiopathiae CWPs proteomes and identified many differences at the protein level. Among the differential proteins with higher abundance in the high-virulence strain, sbp was verified to contribute to the virulence of E. rhusiopathiae through the construction of an sbp-deletion mutant. The differential proteins with higher abundance in the high-virulence strain identified in the present study should provide a foundation for future evaluation of virulence factors.