Identification by PCR signature-tagged mutagenesis of attenuated Salmonella Pullorum mutants and corresponding genes in a chicken embryo model

A key feature of the fowl-specific pathogen Salmonella Pullorum is its vertical transmission to progeny via the egg. In this study, PCR signature-tagged mutagenesis identified nine genes of a strain of S. Pullorum that contributed to survival in the chicken embryo during incubation. The genes were involved in invasion, cell division, metabolism and bacterial defence. The competition index in vivo and in vitro together with a virulence evaluation for chicken embryos of all nine mutant strains confirmed their attenuation

The Global Open Science Cloud: Vision and Initial Successes

The Global Open Science Cloud has the potential to advance the way scientific data and resources are shared and accessed, and how global collaboration happens. However, addressing the challenges associated with its creation and ensuring inclusivity, interoperability, data privacy, and sustainability are crucial for its success. The collaborative efforts of stakeholders from different disciplines, regions, and sectors will be essential in realising the vision of a truly global and open science platform. The achievements of GOSC so far, including successful collaborations, funded projects, and the development of a common reference framework, demonstrate its potential and progress towards its goals

Environmental flow mechanism and management for river–lake-marsh systems

Sustaining environmental flows (e-flows) is a basic requirement for river, lake and marsh management. Rivers, lakes and marshes have close hydrological and ecological connections in a river basin, and form river–lake-marsh systems. Any measure that is designed to address problems related to only one of these water bodies in isolation of the others may lead to unexpected, undesired and sub-optimal consequences for one or all of the water bodies. Papers were selected for this special issue ‘Environmental Flow Mechanism and Management for River-Lake-Marsh Systems’ to illustrate recent advances in revealing new mechanisms connecting hydrological and environmental/ecological processes, developing new methods for e-flow calculation, and establishing new measures for e-flow management

Sustainable Water Resource Management of Regulated Rivers under Uncertain Inflow Conditions Using a Noisy Genetic Algorithm

Ecofriendly reservoir operation is an important tool for sustainable water resource management in regulated rivers. Optimization of reservoir operation is potentially affected by the stochastic characteristics of inflows. However, inflow stochastics are not widely incorporated in ecofriendly reservoir operation optimization. The reasons might be that computational cost and unsatisfactory performance are two key issues for reservoir operation under uncertainty inflows, since traditional simulation methods are usually needed to evaluate over many realizations and the results vary between different realizations. To solve this problem, a noisy genetic algorithm (NGA) is adopted in this study. The NGA uses an improved type of fitness function called sampling fitness function to reduce the noise of fitness assessment. Meanwhile, the Monte Carlo method, which is a commonly used approach to handle the stochastic problem, is also adopted here to compare the effectiveness of the NGA. Degree of hydrologic alteration and water supply reliability, are used to indicate satisfaction of environmental flow requirements and human needs. Using the Tanghe Reservoir in China as an example, the results of this study showed that the NGA can be a useful tool for ecofriendly reservoir operation under stochastic inflow conditions. Compared with the Monte Carlo method, the NGA reduces ~90% of the computational time and obtains higher water supply reliability in the optimization

The Influence of Channel Morphological Changes on Environmental Flow Requirements in Urban Rivers

Previous research on environmental flows (e-flows) of urban rivers usually assumes that the channel morphology is fixed. However, due to the trapping of sediments by weirs, the channel morphology will undergo significant changes. In this research, the influence of channel morphological changes on e-flow requirements is explored in urban rivers. The hydrological connectivity is considered as a primary factor in e-flows, and three hydrological connectivity scenarios (i.e., high, medium, and low) are explored. The Shiwuli River is adopted as the case study. The results show that e-flows are significantly influenced by changes in river morphology. With an increase in siltation depth, the e-flow requirements will decrease. The sensitivity of e-flows to siltation varies among different river segments, especially in those with low weir heights. In addition, the change ratios of e-flows are different under different hydrological connectivity scenarios. Although siltation is beneficial to the satisfaction degree of e-flow supply, it also leads to a decrease in the flood control ability of rivers. The balance between e-flow and flood reduction is also discussed, and river segments are identified that should be the priority when adopting dredging measures

The Salmonella T3SS1 effector IpaJ is regulated by ItrA and inhibits the MAPK signaling pathway

Invasion plasmid antigen J (IpaJ) is a protein with cysteine protease activity that is present in Salmonella and Shigella species. Salmonella enterica serovar Pullorum uses IpaJ to inhibit the NF-κB pathway and the subsequent inflammatory response, resulting in bacterial survival in host macrophages. In the present study, we performed a DNA pull-down assay and EMSA and identified ItrA, a new DeoR family transcriptional regulator that could control the expression of IpaJ by directly binding to the promoter of ipaJ. The deletion of itrA inhibited the transcription of ipaJ in Salmonella. Tn-Seq revealed that two regulators of Salmonella pathogenicity island 1 (SPI-1), namely HilA and HilD, regulated the secretion of IpaJ. The deletion of hilA, hilD or SPI-1 inhibited the secretion of IpaJ in both cultured medium and Salmonella-infected cells. In contrast, the strain with the deletion of ssrB (an SPI-2 regulator-encoding gene) displayed normal IpaJ secretion, indicating that IpaJ is an effector of the SPI-1-encoded type III secretion system (T3SS1). To further demonstrate the role of IpaJ in host cells, we performed quantitative phosphoproteomics and compared the fold changes in signaling molecules in HeLa cells infected with wild-type S. Pullorum C79-13 with those in HeLa cells infected with the ipaJ-deleted strain C79-13ΔpSPI12. Both phosphoproteomics and Western blot analyses revealed that p-MEK and p-ERK molecules were increased in C79-13ΔpSPI12- and C79-13ΔpSPI12-pipaJ(C45A)-infected cells; and Co-IP assays demonstrated that IpaJ interacts with Ras to reduce its ubiquitination, indicating that IpaJ can inhibit the activation of the MAPK signaling pathway. Author summary As a cysteine protease, IpaJ present in both Salmonella and Shigella is delivered into host cells to display its activity. However, the expression and secretion of IpaJ remains unclear. Here, we identified a novel DeoR family transcriptional regulator ItrA controlling the transcription of ipaJ, and demonstrated that the expressed IpaJ is an effector of T3SS1. IpaJ can be secreted into culture supernatant in vitro and host cell in vivo dependent on T3SS1. After injection into host cells, IpaJ can not only inhibit the NF-κB pathway and the subsequent inflammatory response through by suppressing IκBα ubiquitination, but also inhibit the activation of the MAPK signaling pathway through downregulation of p-MEK and p-ERK molecules. In summary, we revealed the molecular mechanism of IpaJ expression and secretion in Salmonella, and demonstrated its role in inhibiting host MAPK signaling pathway