Zwitterionic polysaccharides (ZPSs) are exceptional carbohydrates,carrying both positively charged amine groups and negatively chargedcarboxylates, that can be loaded onto MHC-II molecules to... Show moreZwitterionic polysaccharides (ZPSs) are exceptional carbohydrates,carrying both positively charged amine groups and negatively chargedcarboxylates, that can be loaded onto MHC-II molecules to activateT cells. It remains enigmatic, however, how these polysaccharidesbind to these receptors, and to understand the structural featuresresponsible for this "peptide-like" behavior, well-definedZPS fragments are required in sufficient quantity and quality. Wehere present the first total synthesis of Bacteroidesfragilis PS A1 fragments encompassing up to 12 monosaccharides,representing three repeating units. Key to our successful syntheseshas been the incorporation of a C-3,C-6-silylidene-bridged "ring-inverted"galactosamine building block that was designed to act as an apt nucleophileas well as a stereoselective glycosyl donor. Our stereoselective synthesisroute is further characterized by a unique protecting group strategy,built on base-labile protecting groups, which has allowed the incorporationof an orthogonal alkyne functionalization handle. Detailed structuralstudies have revealed that the assembled oligosaccharides take upa bent structure, which translates into a left-handed helix for largerPS A1 polysaccharides, presenting the key positively charged aminogroups to the outside of the helix. The availability of the fragmentsand the insight into their secondary structure will enable detailedinteraction studies with binding proteins to unravel the mode of actionof these unique oligosaccharides at the atomic level. Show less
Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In... Show moreIncreasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress. Show less
The new connectivity, through mobile phones, social media, and wireless internet, is an agent in social change in the drylands. In this chapter, we present four case studies: the introduction of... Show moreThe new connectivity, through mobile phones, social media, and wireless internet, is an agent in social change in the drylands. In this chapter, we present four case studies: the introduction of mobile apps in Mongolia and Kenya, the role of mobile telephony in the Sahel, and the introduction of online learning in the Negev Desert. Each of these case studies develops an argument around the role of connectivity in ‘giving a voice’ to the people living in drylands. Indeed, as the studies show, the new technology of communication is a resource for such populations, especially when we focus on the benefits of improved communication and access to information. However, the effective use of such a resource is hampered by the lack of knowledge of dryland dynamics among the developers of the new technology and by the imposed power relations of the State. Also, the technology may follow its own pathway, being appropriated by the population in unexpected ways and creating new power relations that may also lead to conflict. Show less
Synthase-dependent secretion systems are a conserved mechanism for producing exopolysaccharides in Gram-negative bacteria. Although widely studied, it is not well understood how these systems are... Show moreSynthase-dependent secretion systems are a conserved mechanism for producing exopolysaccharides in Gram-negative bacteria. Although widely studied, it is not well understood how these systems are organized to coordinate polymer biosynthesis, modification, and export across both membranes and the peptidoglycan. To investigate how synthase-dependent secretion systems produce polymer at a molecular level, we determined the crystal structure of the AlgK-AlgX (AlgKX) complex involved in Pseudomonas aeruginosa alginate exopolysaccharide acetylation and export. We demonstrate that AlgKX directly binds alginate oligosaccharides and that formation of the complex is vital for polymer production and biofilm attachment. Finally, we propose a structural model for the AlgEKX outer membrane modification and secretion complex. Together, our study provides insight into how alginate biosynthesis proteins coordinate production of a key exopolysaccharide involved in establishing persistent Pseudomonas lung infections. Show less
The Russia-Ukraine war has disrupted global food supply chains and driven food prices up in many parts of the world. This study applies a spatially explicit modelling approach to estimate the... Show moreThe Russia-Ukraine war has disrupted global food supply chains and driven food prices up in many parts of the world. This study applies a spatially explicit modelling approach to estimate the resilience and environmental co-benefits of a transition towards the EAT-Lancet's planetary health diets across Europe.Crises related to extreme weather events, COVID-19 and the Russia-Ukraine conflict have revealed serious problems in global food (inter)dependency. Here we demonstrate that a transition towards the EAT-Lancet's planetary health diet in the European Union and the United Kingdom alone would almost compensate for all production deficits from Russia and Ukraine while yielding improvements in blue water use (4.1 Gm(3) yr(-1)), greenhouse gas emissions (0.22 GtCO(2)e yr(-1)) and carbon sequestration (17.4 GtCO(2)e). Show less
Xu, N.; Kang, J.; Ye, Y.; Zhang, Q.; Ke, M.; Wang, Y.; ... ; Qian, H. 2022
With the rapid development of nanotechnology in agriculture, there is increasing urgency to assess the impacts of nanoparticles (NPs) on the soil environment. This study merged raw high-throughput... Show moreWith the rapid development of nanotechnology in agriculture, there is increasing urgency to assess the impacts of nanoparticles (NPs) on the soil environment. This study merged raw high-throughput sequencing (HTS) data sets generated from 365 soil samples to reveal the potential ecological effects of NPs on soil microbial community by means of metadata analysis and machine learning methods. Metadata analysis showed that treatment with nanoparticles did not have a significant impact on the alpha diversity of the microbial community, but significantly altered the beta diversity. Unfortunately, the abundance of several beneficial bacteria, such as Dyella, Methylophilus, Streptomyces, which promote the growth of plants, and improve pathogenic resistance, was reduced under the addition of synthetic nanoparticles. Furthermore, metadata demonstrated that nanoparticles treatment weakened the biosynthesis ability of cofactors, carriers, and vitamins, and enhanced the degradation ability of aromatic compounds, amino acids, etc. This is unfavorable for the performance of soil functions. Besides the soil heterogeneity, machine learning uncovered that a) the exposure time of nanoparticles was the most important factor to reshape the soil microbial community, and b) long-term exposure decreased the diversity of microbial community and the abundance of beneficial bacteria. This study is the first to use a machine learning model and metadata analysis to investigate the relationship between the properties of nanoparticles and the hazards to the soil microbial community from a macro perspective. This guides the rational use of nanoparticles for which the impacts on soil microbiota are minimized. Show less
In the past decades, hundreds of antibiotics have been isolated from microbial metabolites or have been artificially synthesized for protecting humans, animals and crops from microbial infections.... Show moreIn the past decades, hundreds of antibiotics have been isolated from microbial metabolites or have been artificially synthesized for protecting humans, animals and crops from microbial infections. Their everlasting usage results in impacts on the microbial community composition and causes well-known collateral damage to the functioning of microbial communities. Nevertheless, the impact of different antibiotic properties on aquatic microbial communities have so far only poorly been disentangled. Here we characterized the environmental risk of 50 main kinds of antibiotics from 9 classes at a concentration of 10 μg/L for aquatic bacterial communities via metadata analysis combined with machine learning. Metadata analysis showed that the alpha diversity of the bacterial community increased only after treatment with aminoglycoside and β-lactam antibiotics, while its structure was changed by almost all tested antibiotics. The antibiotic treatment also disturbed the functions of the bacterial community, especially with regard to metabolic pathways, including amino acids, cofactors, vitamins, xenobiotics and carbohydrate metabolism. The critical characteristics (atom stereocenter count, number of hydrogen atoms in the antibiotic, and the adipose water coefficient) of antibiotics affecting the composition of the bacterial community in aquatic habitats were screened by machine learning. The key characteristics of antibiotics affecting the function bacterial communities were the number of hydrogen atoms, molecular weight and complexity. In summary, by developing machine learning models and by performing metadata analysis, this study provides the relationship between the properties of antibiotics and their adverse impacts on aquatic microbial communities from a macro perspective. The study also provides guidance for the rational design of antibiotics. Show less
This dissertation studies the construction of Chinese nationalism by the Chinese government and media companies through mass communication of government-staged and abrupt events in the reform era... Show moreThis dissertation studies the construction of Chinese nationalism by the Chinese government and media companies through mass communication of government-staged and abrupt events in the reform era between 2008 and 2012. It examines how Chinese audiences express online nationalist sentiments, representing whether the communication of media events meets the social demands established by “dream discourses.” Using mixed qualitative and quantitative methods, it focuses on two case studies: the 2008 Beijing Olympics and the 2012 Diaoyu (Senkaku) Islands incident. The dissertation finds that these mass media events play a significant role in shaping Chinese state nationalism and popular nationalism. The related mass communication helps the Chinese government increase or, at least, maintain its legitimacy through various strategies. The findings of this dissertation also show that as Chinese audiences have increasingly voiced themselves in the information age, the government will keep treating the robust, uneasy entanglement of nationalism, globalization, and digital media more cautiously for its social development and stability. Show less
The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms.... Show moreThe leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant–microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant–atmosphere interactions, plant pathogens, and plant biological control. Show less
The asymptotic equivalence of canonical and microcanonical ensembles is a central concept in statistical physics, with important consequences for both theoretical research and practical... Show moreThe asymptotic equivalence of canonical and microcanonical ensembles is a central concept in statistical physics, with important consequences for both theoretical research and practical applications. However, this property breaks down under certain circumstances. The most studied violation of ensemble equivalence requires phase transitions, in which case it has a 'restricted' (i.e. confined to a certain region in parameter space) but 'strong' (i.e. characterized by a difference between the entropies of the two ensembles that is of the same order as the entropies themselves) form. However, recent research on networks has shown that the presence of an extensive number of local constraints can lead to ensemble nonequivalence (EN) even in the absence of phase transitions. This occurs in a 'weak' (i.e. leading to a subleading entropy difference) but remarkably 'unrestricted' (i.e. valid in the entire parameter space) form. Here we look for more general manifestations of EN in arbitrary ensembles of matrices with given margins. These models have widespread applications in the study of spatially heterogeneous and/or temporally nonstationary systems, with consequences for the analysis of multivariate financial and neural time-series, multi-platform social activity, gene expression profiles and other big data. We confirm that EN appears in 'unrestricted' form throughout the entire parameter space due to the extensivity of local constraints. Surprisingly, at the same time it can also exhibit the 'strong' form. This novel, simultaneously 'strong and unrestricted' form of nonequivalence is very robust and imposes a principled choice of the ensemble. We calculate the proper mathematical quantities to be used in real-world applications. Show less
Systems with local constraints is a new finding in recent researches on complex systems. The heterogeneous spatial interactions and the temporal dependencies among those numerous units make it... Show moreSystems with local constraints is a new finding in recent researches on complex systems. The heterogeneous spatial interactions and the temporal dependencies among those numerous units make it difficult to describe by traditional statistical physics.These complex structures also make information storage and transmission in it is impossible to describe by the random variables with finite outcomes in the classical information theory. In this thesis, we use the statistical ensemble with local constraints to describe those complex systems with heterogeneous interactions and dependencies. This description also helps us find the new information-theoretical bounds in the systems with local constraints, even when the temporal dependencies among numerous units break the asymptotic equipartition property in the classical information theory.Furthermore, we find that the breaking of ensemble equivalence generally exists in systems with local constraints even without the presence of phase transition, and this ensemble nonequivalence in the systems with local constraints without phase transition can be the same strong as the one that only appears on the boundary of phase transitions caused by the long-range interactions. We also find that this breaking of ensemble equivalence will affect the limit of information storage and transmission in systems with local constraints.These results in this thesis extend our understanding of complex systems and information theory. Show less
Zhan, J.; Lv, F.; Li, Z.; Jiang, G.; Tan, M.; Yuan, M.; ... ; Guo, S. 2021
Electrochemical sensors for detecting micromolecule organics are desirable for improving the perception of environmental quality and human health. However, currently, the electrochemical sensors... Show moreElectrochemical sensors for detecting micromolecule organics are desirable for improving the perception of environmental quality and human health. However, currently, the electrochemical sensors for formaldehyde are substantially limited on the market due to the long-term unsolved problems of the low electrooxidation efficiency and CO poisoning issue of commercial Pd catalysts. Here, a 2D Cr-doped Pd metallene (Cr-Pdene) with few atomic layers is shown as an advanced catalyst for ultrasensitive and selective sensing of formaldehyde via a highly efficient formaldehyde electrooxidation. It is found that the doping of Cr into Pd metallene can efficiently optimize the electronic structure of Pd and weaken the interaction between Pd and CO, providing an anti-poisoning means to favor CO2 production and suppress CO adsorption. The Cr-Pdene-based electrochemical sensor exhibits one order of magnitude higher detection range and, especially, much higher anti-interference for formaldehyde than that of the conventional sensors. Most importantly, it is demonstrated that the Cr-Pdene can be integrated into commercializable wireless sensor networks or handheld instruments for promising applications relating to the environment, health, and food. Show less
Plant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root... Show morePlant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root exudates and provide beneficial functions to their plant host. Whether the biorhythms in plants would transfer to the rhizosphere microbial community is still uncertain and their intricate connection remains poorly understood. Here, we investigated the role of the Arabidopsis circadian clock in shaping the rhizosphere microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101) with transcriptomic, metabolomic and 16S rRNA gene sequencing analysis throughout a 24-h period. Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. The bacterial community failed to follow obvious patterns in the 24-h period, and there was lack of coordination with plant growth in the clock mutants. Our results suggest that the robust rhythmicity of genes and root exudation due to circadian clock in plants is an important driving force for the positive succession of rhizosphere communities, which will feedback on plant development. Show less
