Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity.

The hepatocytes within the liver present an immense capacity to adapt to changes in nutrient availability. Here, by using high resolution volume electron microscopy, we map how hepatic subcellular spatial organization is regulated during nutritional fluctuations and as a function of liver zonation. We identify that fasting leads to remodeling of endoplasmic reticulum (ER) architecture in hepatocytes, characterized by the induction of single rough ER sheet around the mitochondria, which becomes larger and flatter. These alterations are enriched in periportal and mid-lobular hepatocytes but not in pericentral hepatocytes. Gain- and loss-of-function in vivo models demonstrate that the Ribosome receptor binding protein1 (RRBP1) is required to enable fasting-induced ER sheet-mitochondria interactions and to regulate hepatic fatty acid oxidation. Endogenous RRBP1 is enriched around periportal and mid-lobular regions of the liver. In obesity, ER-mitochondria interactions are distinct and fasting fails to induce rough ER sheet-mitochondrion interactions. These findings illustrate the importance of a regulated molecular architecture for hepatocyte metabolic flexibility.

Transition of source/sink processes and fate of ammonium in groundwater along with redox gradients.

Ammonium (NH4+) retention/removal processes in groundwater are of great interest because of the continuous increase in nitrogenous compound loading due to anthropogenic activities. However, the transition of multiple co-occurring transformation processes that determine the fate of NH4+ in groundwater along a redox gradient remains underexplored. We selected a high nitrogen (N) groundwater system in the western Hetao Basin, China, to identify and quantify NH4+ source and sink processes, including mineralization, dissimilatory nitrate reduction to ammonium (DNRA), nitrification, and anammox, to better understand the dynamics of NH4+. Based on redox-sensitive parameters, that is, the oxidation-reduction potential (ORP) and NH4+ and nitrate (NO3-) contents, etc., the groundwater system was classified into three zones from upstream to downstream: zone I (oxidizing), zone II (moderately reducing), and zone III (strongly reducing). Using the 15N tracing technique, we found that NH4+ was mainly produced by mineralization while < 2% was produced by DNRA throughout the study area. Mineralization increased downstream because the supply of biodegradable N-containing compounds was augmented, which created a strong redox gradient to host a serial reaction chain. In zone I, NH4+ was mainly transferred to NO3- via nitrification, whereas in zones II and III, NH4+ was mainly transferred to N2 via anammox. The average NH4+ production/consumption ratios (P/C) in zones I, II, and III were 0.7, 6.9, and 51.1, respectively. Obviously, the NH4+ purification ability can only exceed the supply under aerobic conditions, thus suggesting that NH4+ will accumulate without limitation and be retained in strongly reducing groundwater. The situation of NH4+ accumulation would deteriorate over space and time in groundwater as human activities increase without an additional artificial supply of oxidants. The results provide mechanistic insights for quantitatively comprehending the dynamics and fate of NH4+ in groundwater, shedding light on groundwater NH4+ mitigation techniques.

Diel change in inorganic nitrogenous nutrient dynamics and associated oxygen stoichiometry along the Pearl River Estuary.

The reactive nitrogen (N) emitted from continents significantly perturbs the pristine N cycle around the land-ocean boundary resulting in eutrophication and hypoxia. As nutrients are transported downstream through an estuary, various types of biological processes co-occur to modulate nitrogen speciation to influence the biogeochemical habitats for downstream microorganisms. We surveyed the Pearl River Estuary to examine the N transfer dynamics among nitrogen species with considering process-specific oxygen production and consumption. By using 15N pulse-tracing techniques, we measured ammonia oxidation and uptakes of ammonium, nitrite, and nitrate simultaneously under dark and light conditions in parallel. Light strongly inhibited nitrification but enhanced N uptake, and such light effect was further considered in the calculation for nitrogen transformation rates over a diel cycle. We found both oxidation and uptake of ammonium decreased seaward as substrate decreased. The nitrifier and phytoplankton work in antiphase to draw down incoming ammonium rapidly. Contrary to ammonium uptake, uptake of nitrite and nitrate showed a seaward increasing pattern. Such an inverse spatial pattern implies a shift in N preference for phytoplankton. Such high ammonium preference inhibits nitrate/nitrite uptake allowing them to behave conservatively in the estuary and to travel farther to outer estuary. By integrating oxygen consumption and production induced by N transformation processes over the diel cycle, oxygen was produced although allochthonous ammonium input is high (∼250 µM). For most stations, ammonium was completely consumed within 2 days, some stations even less than 0.5 days, implying that although the water residence time is short (2-15 days), tremendous input of ammonium N from upstream was transformed into particulate organic or nitrate forms during traveling to modulate the biogeochemical niche, including substrate, organics and oxygen, of coastal microbes in water column and sediments.

Regulation of liver subcellular architecture controls metabolic homeostasis.

Cells display complex intracellular organization by compartmentalization of metabolic processes into organelles, yet the resolution of these structures in the native tissue context and their functional consequences are not well understood. Here we resolved the three-dimensional structural organization of organelles in large (more than 2.8 × 105 µm3) volumes of intact liver tissue (15 partial or full hepatocytes per condition) at high resolution (8 nm isotropic pixel size) using enhanced focused ion beam scanning electron microscopy1,2 imaging followed by deep-learning-based automated image segmentation and 3D reconstruction. We also performed a comparative analysis of subcellular structures in liver tissue of lean and obese mice and found substantial alterations, particularly in hepatic endoplasmic reticulum (ER), which undergoes massive structural reorganization characterized by marked disorganization of stacks of ER sheets3 and predominance of ER tubules. Finally, we demonstrated the functional importance of these structural changes by monitoring the effects of experimental recovery of the subcellular organization on cellular and systemic metabolism. We conclude that the hepatic subcellular organization of the ER architecture are highly dynamic, integrated with the metabolic state and critical for adaptive homeostasis and tissue health.

Nitrogen isotope constraint on the zonation of multiple transformations between dissolved and particulate organic nitrogen in the Changjiang plume.

Information on the sources and transformations of particulate organic N (PN) and dissolved organic N (DON) at the coastal interface remains insufficient due to technological difficulties and complicated features of intensive physical mixing and rapid biological activities. Here, we investigated the spatial distribution of concentrations and isotopic compositions of PN and DON in the Changjiang plume during the summer flood period. In average, DON and PN accounted for 25.6 ± 12.1% and 8.1 ± 9.1% (n = 55), respectively, of the total N pool, with the remaining N primarily in the form of nitrate (NO3-). Mean δ15N values were the lowest for DON (-0.1 ± 2.7‰, n = 58) and slightly higher for PN (2.0 ± 1.6‰, n = 101), and the highest for NO3- (6.5 ± 2.2‰, n = 67), suggesting multiple transformations had occurred to differentiate isotopic characteristics among the three N pools. By applying a conservative mixing model, we found DON deficits (-3.5 ± 3.7 µmol L-1, n = 43) and negative shift in δ15NDON (-3.6 ± 2.2‰, n = 43) in the Changjiang plume, revealing nonconservative DON behaviors. In the offshore surface plume where Chlorophyll a was high, the most likely cause is the DON uptake by phytoplankton with a strong inverse isotope effect (around -40‰). This DON assimilation by phytoplankton contributed to ~16 ± 12% of the PN production, with the remaining supported by NO3- assimilation, producing an overall isotope effect of 4-9‰. However, in waters near the river mouth and at the bottom of the offshore plume where total suspended matter concentrations were high (>5 mg L-1), the DON deficit was most likely induced by the selective adsorption of 15N enriched moieties of DON onto particulate surfaces (with an isotope effect of -20‰ to -5‰). Unlike dissolved organic carbon to behave conservatively in most estuaries, our results show that active transformations had occurred between the DON and PN pools in the Changjiang plume.

Aberrant Ca2+ signaling by IP3Rs in adipocytes links inflammation to metabolic dysregulation in obesity.

Chronic metabolic inflammation is a key feature of obesity, insulin resistance, and diabetes. Here, we showed that altered regulation of the Ca2+ channel inositol trisphosphate receptor (IP3R) was an adipocyte-intrinsic event involved in the emergence and propagation of inflammatory signaling and the resulting insulin resistance. Inflammation induced by cytokine exposure in vitro or by obesity in vivo led to increases in the abundance and activity of IP3Rs and in the phosphorylation of the Ca2+-dependent kinase CaMKII in adipocytes in a manner dependent on the kinase JNK. In mice, adipocyte-specific loss of IP3R1/2 protected against adipose tissue inflammation and insulin resistance, despite the mice exhibiting substantial diet-induced weight gain. Thus, this work suggests that increased IP3R activity is a key link between obesity, inflammation, and insulin resistance. These data also suggest that approaches to target IP3R-mediated Ca2+ homeostasis in adipocytes may offer new therapeutic opportunities against metabolic diseases, especially because GWAS studies also implicate this locus in human obesity.

Investigating the link between Pearl River-induced eutrophication and hypoxia in Hong Kong shallow coastal waters.

We present geochemical analysis of 75 surface water samples collected in 2016 in Hong Kong coastal waters. We found that nitrogen distribution around Hong Kong can be characterized by two regimes driven by the influence of the Pearl River: 1) a regime where nitrate is the dominant species of nitrogen, associated with lower salinity and more faecal coliform and 2) a regime where dissolved organic nitrogen is dominant, associated with higher salinity and fewer faecal coliform. While the impact of the Pearl River on Hong Kong coastal waters is well characterized, we used the sharp contrast between the nitrogen regimes to produce new evidence about the role of the Pearl River on the generation of local hypoxia in Hong Kong. The impact of nitrate originating from the Pearl River on the generation of hypoxia in Hong Kong might be less important than previously thought, as no sign of eutrophication was found within the zones dominated by dissolved organic nitrogen and an historical decoupling of surface processes and bottom water oxygenation was observed. Moreover, we measured elevated ammonium levels and rapid cycling of ammonium and dissolved organic nitrogen in Victoria Harbour suggesting local sources, such as wastewater, might be rapidly oxidized and thus play an important role in the consumption of oxygen locally. A first-order calculation highlighted the potential for wastewater to drive the observed seasonal decline in oxygen. Taken together, these evidences suggest that eutrophication might not be the primary driver in the generation of seasonal hypoxia and that oxidation of ammonium released locally might play a bigger role than initially thought.

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming.

In the context of continuously increasing anthropogenic nitrogen inputs, knowledge of how ammonia oxidation (AO) in the ocean responds to warming is crucial to predicting future changes in marine nitrogen biogeochemistry. Here, we show divergent thermal response patterns for marine AO across a wide onshore/offshore trophic gradient. We find ammonia oxidizer community and ambient substrate co-regulate optimum temperatures (Topt), generating distinct thermal response patterns with Topt varying from ≤14 °C to ≥34 °C. Substrate addition elevates Topt when ambient substrate is unsaturated. The thermal sensitivity of kinetic parameters allows us to predict responses of both AO rate and Topt at varying substrate and temperature below the critical temperature. A warming ocean promotes nearshore AO, while suppressing offshore AO. Our findings reconcile field inconsistencies of temperature effects on AO, suggesting that predictive biogeochemical models need to include such differential warming mechanisms on this key nitrogen cycle process.

Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary.

Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.

Nitrogen sources and cycling revealed by dual isotopes of nitrate in a complex urbanized environment.

Elevated nutrient inputs have led to increased eutrophication in coastal marine ecosystems worldwide. An understanding of the relative contribution of different nutrient sources is imperative for effective water quality management. Stable isotope values of nitrate (δ15NNO3-, δ18ONO3-) can complement conventional water quality monitoring programs to help differentiate natural sources of NO3- from anthropogenic inputs and estimate the processes involved in N cycling within an ecosystem. We measured nutrient concentrations, δ15NNO3-, and δ18ONO3- in 76 locations along a salinity gradient from the lower end of the Pearl River Estuary, one of China's largest rivers discharging into the South China Sea, towards the open ocean. NO3- concentrations decreased with increasing salinity, indicative of conservative mixing of eutrophic freshwater and oligotrophic seawater. However, our data did not follow conservative mixing patterns. At salinities <20 psu, samples exhibited decreasing NO3-concentrations with almost unchanged NO3- isotope values, indicating simple dilution. At salinities >20 psu, NO3- concentrations decreased, while dual NO3- isotopes increased, suggesting mixing and/or other transformation processes. Our analysis yielded mean estimates for isotope enrichment factors (15ε = -2.02‰ and 18ε = -3.37‰), Δ(15,18) = -5.5‰ and δ15NNO3- - δ15NNO2- = 12.3‰. After consideration of potential alternative sources (sewage, atmospheric deposition and groundwater) we concluded that there are three plausible interpretations for deviations from conservative mixing behaviour (1) NO3- uptake by assimilation (2) in situ NO3- production (from fixation-derived nitrogen and nitrification of sewage-derived effluents) and (3) input of groundwater nitrate carrying a denitrification signal. Through this study, we propose a simple workflow that incorporates a synthesis of numerous isotope-based studies to constrain sources and behaviour of NO3- in urbanized marine environments.

Catch and Release of Cytokines Mediated by Tumor Phosphatidylserine Converts Transient Exposure into Long-Lived Inflammation.

Immune cells constantly survey the host for pathogens or tumors and secrete cytokines to alert surrounding cells of these threats. In vivo, activated immune cells secrete cytokines for several hours, yet an acute immune reaction occurs over days. Given these divergent timescales, we addressed how cytokine-responsive cells translate brief cytokine exposure into phenotypic changes that persist over long timescales. We studied melanoma cell responses to transient exposure to the cytokine interferon γ (IFNγ) by combining a systems-scale analysis of gene expression dynamics with computational modeling and experiments. We discovered that IFNγ is captured by phosphatidylserine (PS) on the surface of viable cells both in vitro and in vivo then slowly released to drive long-term transcription of cytokine-response genes. This mechanism introduces an additional function for PS in dynamically regulating inflammation across diverse cancer and primary cell types and has potential to usher in new immunotherapies targeting PS and inflammatory pathways.