Impact of Osmotic Stressors on the Metabolic Activity of Methylocystis sp. Strain SC2

Proteobacterial methane-oxidizing bacteria, or methanotrophs, have the unique ability to grow on methane as their sole source of carbon and energy. Among these, Methylocystis spp. belong to the family Methylocystaceae within the Alphaproteobacteria. Their key enzyme is the particulate methane monooxygenase (pMMO), which oxidizes methane to methanol. Methylocystis spp. are among the ecologically most relevant methanotroph populations in terrestrial environments and are widely distributed in diverse habitats. In consequence, Methylocystis spp. require a range of physiological capabilities that allow them to respond and acclimatize to fluctuations in abiotic and biotic factors in their native environment. However, to date there still exist major gaps in our knowledge of their metabolic potential, in particular with regard to their ability to acclimatize to environmental change and to cope with abiotic stress. In my first project, we used a recently developed proteome workflow to elucidate the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to high NH4+ load (added as NH4Cl). Relative to 1 mM NH4+, high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment, while the addition of 100 mM NH4+ completely inhibited growth of strain SC2. The number of differentially regulated proteins was highly significantly correlated to the increase in NH4+ load. The cellular responses involved the significant upregulation of stress-responsive proteins, the K+ “salt-in” strategy, the synthesis of compatible solutes (glutamate and proline), and the glutathione metabolism. The apparent Km value for CH4 oxidation significantly increased with the NH4+ load. This observation was indicative of an increased pMMO-based oxidation of NH3 to toxic hydroxylamine. In consequence, the detoxifying activity of hydroxlyamine oxidoreductase (HAO) increased with the NH4+ concentration and led to a significant accumulation of NO2− and, with delay, N2O. Significant production of N2O occurred only after the oxygen concentration had dropped to low or unmeasurable levels. Thus, high NH4+ load had a dual effect on the activity of strain SC2, with one being general phenomenon of ionic-osmotic stress and the other being the competitive inhibition effect of NH3 on pMMO-based methane oxidation. Although strain SC2 precisely rebalanced enzymes and osmolyte composition in response to the increase in NH4+ load, the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. Starting point of my second project was the knowledge that the growth of strain SC2 is completely inhibited at medium concentrations  1.5% NaCl. Sodium chloride is an important ionic-osmotic stressor in bulk and rhizosphere soils. We therefore tested various amino acids and other osmolytes for their potential to act as a compatible solute or osmoprotectant under otherwise inhibitory NaCl conditions. The addition of 10 mM asparagine to the growth medium had the greatest stress relief effect under severe salinity (1.5% NaCl), leading to a partial growth recovery of strain SC2. The analysis of the exo-metabolome revealed that asparagine was taken up quantitatively by strain SC2. This resulted in an intracellular concentration of 264 ± 57 mM asparagine. Under severe salinity (1.5% NaCl), the uptake of asparagine induced major proteome rearrangements related to the KEGG level 2 categories energy metabolism, amino acid metabolism, and cell growth and death. In particular, various proteins involved in cell division and peptidoglycan synthesis showed a positive expression response. The incorporation of asparagine-derived 13C-carbon into nearly all amino acids indicated that asparagine acted as a source for cell biomass under severe salinity (1.5% NaCl), with glutamate being a major hub between central carbon and amino acid pathways

Qingchang Wenzhong Decoction Attenuates DSS-Induced Colitis in Rats by Reducing Inflammation and Improving Intestinal Barrier Function via Upregulating the MSP/RON Signalling Pathway

Ulcerative colitis (UC) is a chronic, nonspecific, inflammatory disease for which an effective treatment is lacking. Our previous study found that Qingchang Wenzhong Decoction (QCWZD) can significantly improve the clinical symptoms of UC and ameliorate dextran sulphate sodium- (DSS-) induced ulcerative colitis in rats by downregulating the IP10/CXCR3 axis–mediated inflammatory response. The purpose of the present study was to further explore the mechanism of QCWZD for UC in rats models, which were established by 7-day administration of 4.5% dextran sulphate sodium solution. QCWZD was administered daily for 7 days; then we determined the serum macrophage-stimulating protein concentration (MSP) and recepteur d’origine nantais (RON) expression and its downstream proteins (protein kinase B [Akt], phosphorylated [p] Akt, occludin, zona occluden- [ZO-] 1, and claudin-2) in colon tissue using Western blotting and quantitative polymerase chain reaction. In DSS-induced UC, QCWZD significantly alleviated colitis-associated inflammation, upregulated serum MSP expression and RON expression in the colon, reduced the pAkt levels, promoted colonic occluding and ZO-1 expression, and depressed claudin-2 expression. In conclusion, the MSP/RON signalling pathway plays an important role in the pathogenesis of UC by involving the inflammatory response and improving intestinal barrier function. QCWZD appears to attenuate DSS-induced UC in rats by upregulating the MSP/RON signalling pathway

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level

The Effects of Five-Year Biosolid Application on the Diversity and Community of Soil Arthropods

Land application of biosolids is a beneficial form of management, although heavy metal contamination is a major concern. Biosolid application can shape the abundance, species richness, and community structure of arthropods, which are important regulators of soil processes. We investigated the effect of the five-year (2012–2017) application of domestic biosolids at 0, 15, 30, and 45 ton ha−1 on the soil properties, enzyme activity, heavy metal concentrations, abundance, and diversity of soil arthropods in degraded sandy soil. The results showed that the application of a high amount of biosolids resulted in an increase in soil organic carbon of 2.6 times and in the water content of 2.8 times compared with CK (no biosolids). The total metal concentrations of Cr, Ni, Cu, Zn, Cd, and Pb increased by 6.6%, 3.2%, 6.6%, 7.7%, 13.3%, and 22.5%, respectively, compared with CK in soil (p > 0.05). The activities of seven enzymes, which mainly participate in carbon (C), nitrogen (N), phosphate (P), and sulfur (S) transformation, increased by 1.53%~122.7%, indicating that the soil function did not change under biosolid application. The number of individual arthropods collected from a square meter of soil changed from 0 to 2560. The total abundance of arthropods increased from 1.2 to 4 times under biosolid application (p < 0.05), but biosolid application had no effects on simple measures of richness and diversity (Shannon–Weaver index). Multivariate ordination techniques showed a significant shift of the arthropod community structure under biosolid application due to differing responses of several taxa to the biosolids. Redundancy analysis highlighted the influential role of soil chemical properties (soil organic C, total N, water content, microbial biomass, and pH) and cadmium in shaping the soil arthropod structure. These results suggest that long-term biosolid application with limited heavy metal concentrations does not have detrimental effects on soil arthropods or microbial-related soil function

Analysis of the Nonlinear Trends and Non-Stationary Oscillations of Regional Precipitation in Xinjiang, Northwestern China, Using Ensemble Empirical Mode Decomposition

Changes in precipitation could have crucial influences on the regional water resources in arid regions such as Xinjiang. It is necessary to understand the intrinsic multi-scale variations of precipitation in different parts of Xinjiang in the context of climate change. In this study, based on precipitation data from 53 meteorological stations in Xinjiang during 1960–2012, we investigated the intrinsic multi-scale characteristics of precipitation variability using an adaptive method named ensemble empirical mode decomposition (EEMD). Obvious non-linear upward trends in precipitation were found in the north, south, east and the entire Xinjiang. Changes in precipitation in Xinjiang exhibited significant inter-annual scale (quasi-2 and quasi-6 years) and inter-decadal scale (quasi-12 and quasi-23 years). Moreover, the 2–3-year quasi-periodic fluctuation was dominant in regional precipitation and the inter-annual variation had a considerable effect on the regional-scale precipitation variation in Xinjiang. We also found that there were distinctive spatial differences in variation trends and turning points of precipitation in Xinjiang. The results of this study indicated that compared to traditional decomposition methods, the EEMD method, without using any a priori determined basis functions, could effectively extract the reliable multi-scale fluctuations and reveal the intrinsic oscillation properties of climate elements

Effects of Different Fertilization Methods on Double-Rice Yield and Bacterial Community in Paddy Soil

Fertilizer regimes have profound effects on crop yield, soil fertility, and microbial community structure. However, the impacts of partially substituting mineral nitrogen (N) with organic N and/or controlled-release mineral N and combining with micronutrient fertilizers on soil properties and microbial communities are still unclear in double-rice systems. The objective of this study was to compare rice yield, soil nutrient condition, and bacterial alpha and beta diversity in paddy soil that had been subjected to four fertilizer treatments from 2012 to 2016. The treatments were FP: farmers’ practice with 100% urea N; T1: 64% urea N + 16% manure N; T2: T1 + micronutrient fertilizers; and T3: 40% urea N + 24% controlled-release N + 16% manure N + micronutrient fertilizers. The results showed that there were no considerable differences between rice yields under fertilizer treatments, meaning that reducing farmers’ practice N by 20% did not decrease rice yield. Soil organic matter, total N, pH, and microbial biomass receiving manure did not increase significantly compared with FP. Bacterial beta diversities did not alter under the four treatments. Only two (Verrucomicrobia and Aminicenantes) out of eleven dominant phyla considerably varied under manure treatments. These results indicate that 20% reduction and partial substitution of mineral fertilizer with manure can maintain double-rice yield in paddy soil with limited effects on soil properties and bacterial community structure

Engineering placenta‐like organoids containing endogenous vascular cells from human‐induced pluripotent stem cells

Abstract The placenta is an essential organ that maintains the health of both the fetus and its mother. Understanding the development of human placenta has been hindered by the limitations of existing animal models and monolayer cell cultures. Models that can recapitulate the essential aspects of human placental multicellular components and vasculature are still lacking. Herein, we presented a new strategy to establish placenta‐like organoids with vascular‐like structures from human‐induced pluripotent stem cells in a defined three‐dimensional (3D) culture system. The resulting placenta‐like tissue resembles first‐trimester human placental development in terms of complex placental components and secretory function. The multicellular tissue was characterized by the inclusion of trophoblasts (cytotrophoblasts, syncytiotrophoblasts, extravillous trophoblasts, and other endogenous vascular cells), which were identified by immunofluorescence, flow cytometry analyses, real‐time quantitative reverse transcription polymerase chain reaction and single‐cell RNA‐seq. Moreover, the 3D tissue was able to secrete the placenta‐specific hormone human chorionic gonadotropin β (hCG‐β) and vascular endothelial growth factor A (VEGFA). The tissue responded to the inflammatory factor tumor necrosis factor‐α (TNF‐α) and VEGF receptor inhibitors. This new model system can represent the major features of placental cellular components, and function, which have not been realized in 2D monolayer cultures. The developed tissue system might open new avenues for studying normal early human placental development and its disease states

Advances in Hydrogels in Organoids and Organs-on-a-Chip

Significant advances in materials, microscale technology, and stem cell biology have enabled the construction of 3D tissues and organs, which will ultimately lead to more effective diagnostics and therapy. Organoids and organs-on-a-chip (OOC), evolved from developmental biology and bioengineering principles, have emerged as major technological breakthrough and distinct model systems to revolutionize biomedical research and drug discovery by recapitulating the key structural and functional complexity of human organs in vitro. There is growing interest in the development of functional biomaterials, especially hydrogels, for utilization in these promising systems to build more physiologically relevant 3D tissues with defined properties. The remarkable properties of defined hydrogels as proper extracellular matrix that can instruct cellular behaviors are presented. The recent trend where functional hydrogels are integrated into organoids and OOC systems for the construction of 3D tissue models is highlighted. Future opportunities and perspectives in the development of advanced hydrogels toward accelerating organoids and OOC research in biomedical applications are also discussed

Effects of Temperature on Transparent Exopolymer Particle Production and Organic Carbon Allocation of Four Marine Phytoplankton Species

Transparent exopolymer particles (TEP) are sticky polymeric substances that are commonly found in the periphery of microbial cells or colonies. They can naturally flocculate smaller suspended particles into larger aggregates and thus play a crucial role in the biological pump and the global carbon cycle. Phytoplankton are the major contributors to marine TEP production, whereas the way TEP production interacts with abiotic factors at the species level is generally unknown but critical for estimating carbon fluxes. In this study, the effects of temperature on TEP production and carbon allocation were studied in two representative diatom species (Nitzschia closterium and Chaetoceros affinis) and two model dinoflagellate species (Prorocentrum micans and Scrippisella trichoidea). The results showed that temperature had a significant impact on TEP production in all species. First, increased temperature promoted the TEP production of all four species. Second, elevated temperature affected the carbon pool allocation, with enhanced dissolved organic carbon (DOC) exudation in the form of TEP in all species. The TEP-C/DOC percentages of N. closterium and P. micans were 93.42 &plusmn; 5.88% and 82.03 &plusmn; 21.36% at the highest temperature (24 &deg;C), respectively, which was approximately two to five times higher than those percentages at 16 &deg;C. In contrast, TEP&rsquo;s contribution to the POC pool is lower than that to the DOC pool, ranging from 6.74 &plusmn; 0.79% to 28.31 &plusmn; 1.79% for all species. Moreover, phytoplankton TEP production may be related to cellular size and physiology. The TEP content produced by the smallest N. closterium (218.96 &plusmn; 15.04 fg Xeq./&mu;m3) was ~5 times higher compared to P. micans, S. trichoidea, or C. affinis. In conclusion, TEP production is temperature sensitive and species specific, which should be taken into consideration the regarding TEP-mediated oceanic carbon cycle, particularly in the context of global warming

Supplemental Figures

Guo et al. Supplementary figures</p