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Ykt6 is an evolutionarily conserved SNARE protein regulating Golgi membrane fusion and other diverse membrane trafficking pathways. Unlike most SNARE proteins, Ykt6 lacks a transmembrane domain but instead has a tandem cysteine motif at the C-terminus. Recently, we have demonstrated that Ykt6 undergoes double prenylation at the C-terminal two cysteines first by farnesyltransferase and then by a newly identified protein prenyltransferase named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of a novel α subunit prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of Rab geranylgeranyltransferase. PTAR1 knockout (KO) cells, where Ykt6 is singly prenylated with a farnesyl moiety, exhibit structural and functional abnormalities in the Golgi apparatus with delayed intra-Golgi trafficking and impaired protein glycosylation. It remains unclear whether the second prenylation of Ykt6 is required for proper trafficking of lysosomal hydrolases from Golgi to lysosomes. Here, we show that lysosomal hydrolases, cathepsin D and β-hexosaminidase, were missorted at the trans-Golgi network and secreted into the extracellular space in PTAR1 KO cells. Moreover, maturation of these hydrolases was disturbed. LC3B, an autophagy marker, was accumulated in PTAR1 KO cells, suggesting defects in cellular degradation pathways. Thus, doubly prenylated Ykt6, but not singly prenylated Ykt6, is critical for the efficient sorting and trafficking of acid hydrolases to lysosomes.

Suspended particulate matter (SPM) in large rivers is the main source of material into delta river ecosystems and the world’s oceans, and is the primary carrier of heavy metals. Large rivers are therefore important sources of pollutant transport through the watershed and potentially alter natural riverine biogeochemical cycling. Asian mega-deltas are some of the most densely populated and urbanizing environments in the world, with pollution, erosion, and anthropogenic catchment modifications changing sediment fluxes and pollutant transport across their catchments. The River Delta (RRD), northern Vietnam, comprises 14,300 km2, making it the fourth largest delta in Southeast Asia. The area has a large population of >22 million and has seen a rapid increase in industry and agriculture with waste products from domestic activities, agriculture, and industry entering the river network often unregulated and untreated. To estimate the impacts of industrialisation in the RRD delta, we measured downriver suspended sediment and pollutant flux from 21 locations over a 17 month period from March 2018 to July 2019. Previous studies suggest sediment retention in the RRD, which is supported here in 2019 with ~30% of sediments retained in the delta. Increased precipitation in 2018, however, led to a ~40% increase in sediment delivery between the inlet and the outlets of the delta, most likely attributed to erosion. Anthropogenic contaminant loads between the inlet and outlets suggest the retention of heavy metals within the delta irrespective of the sediment flux (e.g. a reduction by ~4 and ~14% of SPM bound Cr between sites in 2018 and 2019). This may, in part, be due to spatial variations across the delta revealing ‘hotspots’ of pollution, with a progressive increase in the Cr concentration of SPM between Son Tay (a predominantly agricultural landscape) and Hanoi (a major industrialised urban area) suggesting domestic and industrial waste are major sources of heavy metal pollution. XRF data from upstream Hoa Binh reservoir sediment cores (collected 2017) will permit a comparison of background contaminant storage in the RRD catchment, to better quantify downstream impacts of anthropogenic activity as well as underpin the effects of impoundments on sediment export from the riverine system. Results highlight the role of deltas in ‘filtering’ contaminants to protect coastal areas, but the retention of high loads of pollutants also has potential consequences for the bioaccumulation of heavy metals through the food chain and could ultimately have severe consequences for aquatic and human health in these areas.

Remediation of nitrate pollution of Earth’s rivers and aquifers is hampered by cumulative biogeochemical processes and nitrogen sources. Isotopes (δ15N, δ18O) help unravel spatiotemporal nitrogen(N)-cycling of aquatic nitrate (NO3−). We synthesized nitrate isotope data (n = ~5200) for global rivers and shallow aquifers for common patterns and processes. Rivers had lower median NO3− (0.3 ± 0.2 mg L−1, n = 2902) compared to aquifers (5.5 ± 5.1 mg L−1, n = 2291) and slightly lower δ15N values (+7.1 ± 3.8‰, n = 2902 vs +7.7 ± 4.5‰, n = 2291), but were indistinguishable in δ18O (+2.3 ± 6.2‰, n = 2790 vs +2.3 ± 5.4‰, n = 2235). The isotope composition of NO3− was correlated with water temperature revealing enhanced N-cascading in warmer climates. Seasonal analyses revealed higher δ15N and δ18O values in wintertime, suggesting waste-related N-source signals are better preserved in the cold seasons. Isotopic assays of nitrate biogeochemical transformations are key to understanding nitrate pollution and to inform beneficial agricultural and land management strategies.

Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.

In this study, air, water, and host rock in show caves in a Vietnam’s karst region was monitored and analyzed to identify the ventilation regime and track the cave air CO2 sources. In general, the studied caves are well ventilated. In dynamic – multiple entrance caves, air ventilation is described with the use of U shape model. In static – single entrance cave, air circulation is explained by cold air trap model. Both ventilation models suggest that air is more circulated in winter than in summer. Seasonally, the cave air CO2 increases from early spring to summer. Value in the deepest part of the single-entrance cave is approximately 1,000 ppmv and 8,000 ppmv in early spring and summer, respectively. In multiple-entrance and wet caves, CO2 level is fairly constant all over the show section, increasing from 500 ppmv in early spring to 2,000 ppmv in summer. Data of microclimate, CO2 content, and particularly δ13C show that cave air, particularly in single entrance cave, has higher CO2 concentration during summer due to a stagnation of cave air circulation and an elevated CO2 input from soil and epikarst. The cave air CO2 increase is also observed after intense rainfalls. A factor that increase cave air CO2 in show caves during the festive days could probably be huma n exhaling but the extent of human factor in these studied cave systems should be further investigated. Cave waters including cave pools and streams mediate CO2 level in wet caves. Above all, the atmospheric fraction of CO2 is always dominant (>60%) in all cave sections.

Hai Duong is a rapidly urbanizing province with a condensed network of rivers, located downstream of the Cau River Basin, one of the three most polluted river systems in Vietnam. Intensive agriculture and industrial development in the province has caused profound impact on the river water. This research aims to develop a material flow analysis (MFA) model, which can simulate and visualize nitrogen flows in Hai Duong province and its districts, to access the impact of agricultural activities and industrial parks on the surrounding environments. MFA was applied for Hai Duong province and its districts to estimate nitrogen flows in the whole province. The nitrogen loads to surface water, air, and soil/groundwater annually were 50,531 ± 10,801, 12,981 ± 1541, and 6055 ± 3121 tons, respectively. The quality of the developed model was assessed through a modified uncertainty analysis procedure. Also, MFA results of nitrogen loads to the water environment were consistent with the analytical results. Nitrogen was largely derived from agricultural activities and domestic and industrial wastewater. Environmental flows in the next 10 years and reasonable solutions for improving environmental quality in the province are proposed.

Ribosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.

This paper presents an experiment on lampenflora removal in show caves located in a tropical monsoon climate in southeast Asia. Lampenflora thrive in wet conditions on surfaces directly illuminated by white light. They colonize different levels in show caves, from the cave ceiling, with a biota characterized of mainly cyanobacteria (Oscillatoria, Spirulina), algae (Chlorella, Oedoclarium), and mosses (Cyathodium, Thuidium), to near the cave floor, with a more complex biota including higher plants like ferns (Asplenium) and flowering plants (Centella). Mature lampenflora mats also harbor non-phototrophic fungi and bacteria. With the use of environmental scanning electron microscopy, speleothem surfaces were found severely damaged by lampenflora and their associates. In this study, we used H2O2 as an environmentally friendly chemical to exterminate lampenflora. The applied solution should be at least 15% H2O2 to efficiently destroy microbiota such as green algae, diatoms, and bacteria. For a complex community including mosses, fungi, and vascular plants, repeated spraying of chemical and, if possible, water jet washing at carefully selected places are required to recover the aesthetic characteristics of speleothems. Only a combination of such cleaning practices, and then some modification of the illumination regime, can minimize lampenflora development in show caves.

Background and purpose: Upon stimulation, neutrophils release their nuclear contents called neutrophil extracellular traps (NETs), which contain unfolded chromatin and lysosomal enzymes. NETs have been demonstrated to play a critical role in host defence, although the role of PGE2 , a bioactive substance generated in inflammatory tissues, in the formation of NETs remains unclear. Experimental approach: The effects of PGE2 , agonists and antagonists of its receptors, and modulators of the cAMP-PKA pathway on the formation of NETs were examined in vitro in isolated neutrophils and in vivo in a newly established mouse model. Key results: PGE2 inhibited PMA-induced NET formation in vitro through EP2 and EP4 Gαs-coupled receptors. Incubation with a cell-permeable cAMP analogue, dibutyryl cAMP, or various inhibitors of a cAMP-degrading enzyme, PDE, also suppressed NET formation. In the assay established here, where an agarose gel was s.c. implanted in mice and NET formation was detected on the surface of the gel, the extent of the NET formed was inhibited in agarose gels containing rolipram, a PDE4 inhibitor, and butaprost, an EP2 receptor agonist. Conclusions and implications: PGE2 inhibits NET formation through the production of cAMP. These findings will contribute to the development of novel treatments for NETosis-related diseases.

International audience; Plankton are a major component of food web structure in aquatic ecosystems. Their distribution and community structure are driven by the combination and interactions between physical, chemical, and biological factors within the environment. In the present study, water quality and the community structure of phytoplankton and zooplankton were monthly investigated from January to December 2015 at 11 sampling sites along the gradient course of the Day River (Red River Delta, northern Vietnam). The study demonstrated that the Day River was eutrophic with the average values of total phosphorus concentration 0.17 mg/L, total nitrogen concentration 1.98 mg/L, and Chl a 54 mu g/L. Microscopic plankton analysis showed that phytoplankton comprised 87 species belonging to seven groups in which Chlorophyceae, Bacillariophyceae, and Cyanobacteria accounted for the most important constituents of the river's phytoplankton assemblage. A total 53 zooplankton species belonging to three main groups including Copepoda, Cladocera, and Rotatoria were identified. Plankton biomass values were greatest in rainy season (3002.10-3 cell/L for phytoplankton and 12.573 individuals/m(3) for zooplankton). Using principal correspondence and Pearson correlation analyses, it was found that the Day River was divided into three main site groups based on water quality and characteristics of plankton community. Temperature and nutrients (total phosphorus and total nitrogen) are key factors regulating plankton abundance and distribution in the Day River.

Nitrogen flows impacted by human activities in the Day-Nhue River Basin in northern Vietnam have been modeled using adapted material flow analysis (MFA). This study introduces a modified uncertainty analysis procedure and its importance in MFA. We generated a probability distribution using a Monte Carlo simulation, calculated the nitrogen budget for each process and then evaluated the plausibility under three different criterion sets. The third criterion, with one standard deviation of the budget value as the confidence interval and 68% as the confidence level, could be applied to effectively identify hidden uncertainties in the MFA system. Sensitivity analysis was conducted for revising parameters, followed by the reassessment of the model structure by revising equations or flow regime, if necessary. The number of processes that passed the plausibility test increased from five to nine after reassessment of model uncertainty with a greater model quality. The application of the uncertainty analysis approach to this case study revealed that the reassessment of equations in the aquaculture process largely changed the results for nitrogen flows to environments. The significant differences were identified as increased nitrogen load to the atmosphere and to soil/groundwater (17% and 41%, respectively), and a 58% decrease in nitrogen load to surface water. Thus, modified uncertainty analysis was considered to be an important screening system for ensuring quality of MFA modeling.

International audience; Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible.

Upon stimulation, neutrophils release their nuclear contents called neutrophil extracellular traps (NETs), which contain unfolded chromatin and lysosomal enzymes. NETs have been demonstrated to play a critical role in host defence, although the role of PGE2 , a bioactive substance generated in inflammatory tissues, in the formation of NETs remains unclear.The effects of PGE2 , agonists and antagonists of its receptors, and modulators of the cAMP-PKA pathway on the formation of NETs were examined in vitro in isolated neutrophils and in vivo in a newly established mouse model.PGE2 inhibited PMA-induced NET formation in vitro through EP2 and EP4 Gαs-coupled receptors. Incubation with a cell-permeable cAMP analogue, dibutyryl cAMP, or various inhibitors of a cAMP-degrading enzyme, PDE, also suppressed NET formation. In the assay established here, where an agarose gel was s.c. implanted in mice and NET formation was detected on the surface of the gel, the extent of the NET formed was inhibited in agarose gels containing rolipram, a PDE4 inhibitor, and butaprost, an EP2 receptor agonist.PGE2 inhibits NET formation through the production of cAMP. These findings will contribute to the development of novel treatments for NETosis-related diseases.

International audience; The impact of organic matter inputs from agricultural, forest and domestic sources on aquatic processes has been considerably less studied in tropical reservoirs relative to temperate systems despite the high number of these small aquatic systems in the tropics. Here we present the results of an in situ mesocosm study that examined the impact of allochthonous organic matter on a headwater reservoir in Northern Vietnam. We examined the impact of wastewater and soils from floodplain paddies, Acacia mangium plantations and from upland slopes on the metabolic status of the reservoir. The addition of floodplain paddy soils to the reservoir water led to a rapid switch in metabolic status from net autotrophic to net heterotrophic. In contrast, the addition of wastewater in low concentrations had less impact on the metabolic status of the reservoir, reflecting the low population density in the area. The addition of floodplain paddy soils also increased phytoplankton diversity and evenness relative to the control. In summary, soils from floodplain paddies and from A. mangium plantations had the highest impact on the reservoir, with upland soils and wastewater having less of an impact. We also found that primary production in this reservoir was nitrogen limited. In order to avoid accelerating the impact of runoff on the reservoir, future management options should perhaps focus on minimizing water and sediment runoff from upstream paddy fields and from A. mangium plantations. These results also underline the importance of studying these upland tropical water bodies that can contribute an important but, on the whole, ignored part of the global carbon balance.