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Carbon tetrachloride (CCl4) is an ozone-depleting substance, accounting for about 10% of the chlorine in the troposphere. Under the terms of the Montreal Protocol, its production for dispersive uses was banned from 2010. In this work we show that, despite the controls on production being introduced, CCl4 emissions from the eastern part of China did not decline between 2009 and 2016. This finding is in contrast to a recent bottom-up estimate, which predicted a significant decrease in emissions after the introduction of production controls. We find eastern Asian emissions of CCl4 to be 16 (9-24) Gg/year on average between 2009 and 2016, with the primary source regions being in eastern China. The spatial distribution of emissions that we derive suggests that the source distribution of CCl4 in China changed during the 8-year study period, indicating a new source or sources of emissions from China's Shandong province after 2012.

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01-1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2023. Published by Elsevier Inc. All rights reserved.)

Organic matter has long been understood to affect fine sediment flocculation, yet the specific effects of different types of organic matter remain only partially understood. To address this knowledge gap, laboratory tank experiments were conducted in fresh water to investigate the sensitivity of kaolinite flocculation to varying organic matter species and contents. Three species of organic matter (xanthan gum, guar gum and humic acid) were investigated at varying concentrations. Results revealed a significant enhancement in kaolinite flocculation when organic polymers (xanthan gum and guar gum) were introduced. In contrast, the addition of humic acid had minimal influence on aggregation and floc structure. Notably, the nonionic polymer guar gum demonstrated greater efficacy in promoting the development of floc size compared to the anionic polymer, xanthan gum. We observed non-linear trends in the evolution of mean floc size (Dm) and boundary fractal dimension (N p ) with increasing ratios of organic polymer concentration to kaolinite concentration. Initially, increasing polymer content facilitated the formation of larger and more fractal flocs. However, beyond a certain threshold, further increases in polymer content hindered flocculation and even led to the break-up of macro-flocs, resulting in the formation of more spherical and compact flocs. We further quantified the co-relationships between floc N p and Dm and found that larger N p values corresponded to larger Dm. These findings highlight the significant impact of organic matter species and concentrations on floc size, shape and structure, and shed light on the complex dynamics of fine sediment and associated nutrients and contaminants in fluvial systems., Competing Interests: Declaration of competing interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other interest of any nature or kind in any product, service and/or company that could be constructed as influencing the position presented in, or the review of, the MS entitled., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Many aquatic environments contain cohesive sediments that flocculate and create flocs with a wide range of sizes. The Population Balance Equation (PBE) flocculation model is designed to predict the time-dependent floc size distribution and should be more complete than models based on median floc size. However, a PBE flocculation model includes many empirical parameters to represent important physical, chemical, and biological processes. We report a systematic investigation of key model parameters of the open-source PBE-based size class flocculation model FLOCMOD (Verney, Lafite, Claude Brun-Cottan and Le Hir, 2011) using the measured temporal floc size statistics reported by Keyvani and Strom (2014) at a constant turbulent shear rate S. Results show that the median floc size d 50 , in terms of both the equilibrium floc size and the initial floc growth, is insufficient to constrain the model parameters. A comprehensive error analysis shows that the model is capable of predicting three floc size statistics d 16 , d 50 and d 84 , which also reveals a clear trend that the best calibrated fragmentation rate (inverse of floc yield strength) is proportional to the floc size statistics considered. Motivated by this finding, the importance of floc yield strength is demonstrated in the predicted temporal evolution of floc size by modeling the floc yield strength as microflocs and macroflocs giving two corresponding fragmentation rates. The model shows a significantly improved agreement in matching the measured floc size statistics., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper, (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Cohesive sediment forms flocs of various sizes and structures in the natural turbulent environment. Understanding flocculation is critical in accurately predicting sediment transport and biogeochemical cycles. In addition to aggregation and breakup, turbulence also reshapes flocs toward more stable structures. An Eulerian-Lagrangian framework has been implemented to investigate the effect of turbulence on flocculation by capturing the time-evolution of individual flocs. We have identified two floc reshaping mechanisms, namely breakage-regrowth and restructuring by hydrodynamic drag. Surface erosion is found to be the primary breakup mechanism for strong flocs, while fragile flocs tend to split into fragments of similar sizes. Aggregation of flocs of sizes comparable to or greater than the Kolmogorov scale is modulated by turbulence with lower aggregation efficiency. Our findings highlight the limiting effects of turbulence on both floc size and structure., (© 2023. The Author(s).)

Flocculated suspended sediments (flocs) are found in a variety of environments globally, and their transport and behavior bear substantial importance to several industries including fisheries, aquaculture, and shipping. Additionally, the modelling of their behavior is important for estuarine and coastal flood prediction and defence, and the process of flocculation occurs in other unrelated industries such as paper and chemical production. Floc porosity is conventionally assessed using inferential indirect or proxy data approaches. These methods underestimate floc porosity % by c. 30% and cannot measure the micro-scale complexity of these pore spaces and networks, rendering inputs to models sub-optimal. This study introduces a novel 3D porosity and pore space quantification protocol, that produces directly quantified porosity % and pore space data.•3D floc data from micro-CT scanning is segmented volumetrically•This segmented volume is quantified to extract porosity and several pore space parameters from the floc structure., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

Natural sediment flocs are fragile and highly heterogeneous aggregates of biogenic and minerogenic material typically with high porosity and low density. In aquatic environments dominated by fine, cohesive or mixed sediments they can dominate suspended sediment flux. Consequently, monitoring and modelling the behaviour, transport and distribution of flocs is very important for many aquatic industries, maintenance of waterways and conservation and management of aquatic waterbodies. Mathematical models that predict the behaviour of flocs rely on the accurate assessments of the size, shape, density, porosity and fractal dimension of flocs. These inherently 3-dimensional (3D) characteristics are typically derived from 2-dimensional (2D) data, largely due to the challenges associated with sampling, capturing, imaging and quantifying these fragile aggregates. We have developed new volumetric microscopy techniques which can quantify 3D internal and external structures and characteristics of sediment flocs. Here, these techniques were applied to quantify the 3D size (volume), shape and fractal dimension of natural and artificial sediment flocs and compare them to standard 2D approaches. Our study demonstrates that 2D approaches are under-estimating shape complexity and over-estimating the size and mass settling flux of flocs by up to two orders of magnitude, and the discrepancy between 2D and 3D is most marked for natural, organic rich macroflocs. Our study has significant implications for estimations of sediment flux at local to global scales within in aquatic environments. These new data and approaches offer the potential to improve the current parameterisation of sediment transport models and to improve the accuracy of current field-monitoring techniques., (Copyright © 2022. Published by Elsevier Ltd.)

Global emissions of the ozone-depleting gas HCFC-141b (1,1-dichloro-1-fluoroethane, CH 3 CCl 2 F) derived from measurements of atmospheric mole fractions increased between 2017 and 2021 despite a fall in reported production and consumption of HCFC-141b for dispersive uses. HCFC-141b is a controlled substance under the Montreal Protocol, and its phase-out is currently underway, after a peak in reported consumption and production in developing (Article 5) countries in 2013. If reported production and consumption are correct, our study suggests that the 2017-2021 rise is due to an increase in emissions from the bank when appliances containing HCFC-141b reach the end of their life, or from production of HCFC-141b not reported for dispersive uses. Regional emissions have been estimated between 2017-2020 for all regions where measurements have sufficient sensitivity to emissions. This includes the regions of northwestern Europe, east Asia, the United States and Australia, where emissions decreased by a total of 2.3 ± 4.6 Ggyr -1 , compared to a mean global increase of 3.0 ± 1.2 Ggyr -1 over the same period. Collectively these regions only account for around 30% of global emissions in 2020. We are not able to pinpoint the source regions or specific activities responsible for the recent global emission rise., Competing Interests: Competing interests. The contact author has declared that none of the authors has any competing interests.

With the successful implementation of the Montreal Protocol on Substances that Deplete the Ozone Layer, the atmospheric abundance of ozone-depleting substances continues to decrease slowly and the Antarctic ozone hole is showing signs of recovery. However, growing emissions of unregulated short-lived anthropogenic chlorocarbons are offsetting some of these gains. Here, we report an increase in emissions from China of the industrially produced chlorocarbon, dichloromethane (CH 2 Cl 2 ). The emissions grew from 231 (213-245) Gg yr -1 in 2011 to 628 (599-658) Gg yr -1 in 2019, with an average annual increase of 13 (12-15) %, primarily from eastern China. The overall increase in CH 2 Cl 2 emissions from China has the same magnitude as the global emission rise of 354 (281-427) Gg yr -1 over the same period. If global CH 2 Cl 2 emissions remain at 2019 levels, they could lead to a delay in Antarctic ozone recovery of around 5 years compared to a scenario with no CH 2 Cl 2 emissions., (© 2021. The Author(s).)

The impacts of the partitioning of potentially toxic metals (PTM) within the estuarine environment is highly complex, but is of key significance owing to increases in populations living within such sensitive environments. Although empirical data exist for the partitioning of metals between the dissolved and particulate phases, little is known regarding the impacts of extracellular polymeric substances (EPS) upon the flocculation of particles within such a dynamic system nor the resultant influence on the distribution of metals between the particulate and dissolved phases. This prevents regulators from fully understanding the fate and risks associated with metals in estuaries. This study provides data associated with the simulation of 3 settlings typical of the turbulent mixing found in estuaries and partitioning of copper, cadmium, nickel, arsenic, lead and zinc for 3 salinities (0, 15, 30 PSU) reflecting the full salinity range from freshwater to seawater. Experiments were completed with and without the presence of EPS, using kaolin as the mineral particulate. The results showed significant differences between salinity, PTMs and turbulence for the experiments with and without EPS present. Overall, salinity was the main factor controlling the PTM partitioning to sediment, however the flocculation process did impact on the PTM distribution and with the addition of EPS the impact was more pronounced. The data highlighted the importance of taking account of EPS within any estuarine sediment process modelling, for relying on simple partitioning with corrections for salinity would likely lead to significant bias., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The plant pathogen Pseudomonas syringae secretes multiple effectors that modulate plant defenses. Some effectors trigger defenses due to specific recognition by plant immune complexes, whereas others can suppress the resulting immune responses. The HopZ3 effector of P. syringae pv. syringae B728a (PsyB728a) is an acetyltransferase that modifies not only components of plant immune complexes, but also the Psy effectors that activate these complexes. In Arabidopsis, HopZ3 acetylates the host RPM1 complex and the Psy effectors AvrRpm1 and AvrB3. This study focuses on the role of HopZ3 during tomato infection. In Psy-resistant tomato, the main immune complex includes PRF and PTO, a RIPK-family kinase that recognizes the AvrPto effector. HopZ3 acts as a virulence factor on tomato by suppressing AvrPto1Psy-triggered immunity. HopZ3 acetylates AvrPto1Psy and the host proteins PTO, SlRIPK and SlRIN4s. Biochemical reconstruction and site-directed mutagenesis experiments suggest that acetylation acts in multiple ways to suppress immune signaling in tomato. First, acetylation disrupts the critical AvrPto1Psy-PTO interaction needed to initiate the immune response. Unmodified residues at the binding interface of both proteins and at other residues needed for binding are acetylated. Second, acetylation occurs at residues important for AvrPto1Psy function but not for binding to PTO. Finally, acetylation reduces specific phosphorylations needed for promoting the immune-inducing activity of HopZ3's targets such as AvrPto1Psy and PTO. In some cases, acetylation competes with phosphorylation. HopZ3-mediated acetylation suppresses the kinase activity of SlRIPK and the phosphorylation of its SlRIN4 substrate previously implicated in PTO-signaling. Thus, HopZ3 disrupts the functions of multiple immune components and the effectors that trigger them, leading to increased susceptibility to infection. Finally, mass spectrometry used to map specific acetylated residues confirmed HopZ3's unusual capacity to modify histidine in addition to serine, threonine and lysine residues., Competing Interests: The authors have declared that no competing interests exist.

Natural sediment flocs are fragile, highly irregular, loosely bound aggregates comprising minerogenic and organic material. They contribute a major component of suspended sediment load and are critical for the fate and flux of sediment, carbon and pollutants in aquatic environments. Understanding their behaviour is essential to the sustainable management of waterways, fisheries and marine industries. For several decades, modelling approaches have utilised fractal mathematics and observations of two dimensional (2D) floc size distributions to infer levels of aggregation and predict their behaviour. Whilst this is a computationally simple solution, it is highly unlikely to reflect the complexity of natural sediment flocs and current models predicting fine sediment hydrodynamics are not efficient. Here, we show how new observations of fragile floc structures in three dimensions (3D) demonstrate unequivocally that natural flocs are non-fractal. We propose that floc hierarchy is based on observations of 3D structure and function rather than 2D size distribution. In contrast to fractal theory, our data indicate that flocs possess characteristics of emergent systems including non-linearity and scale-dependent feedbacks. These concepts and new data to quantify floc structures offer the opportunity to explore new emergence-based floc frameworks which better represent natural floc behaviour and could advance our predictive capacity.

The atmospheric concentration of trichlorofluoromethane (CFC-11) has been in decline since the production of ozone-depleting substances was phased out under the Montreal Protocol 1,2 . Since 2013, the concentration decline of CFC-11 slowed unexpectedly owing to increasing emissions, probably from unreported production, which, if sustained, would delay the recovery of the stratospheric ozone layer 1-12 . Here we report an accelerated decline in the global mean CFC-11 concentration during 2019 and 2020, derived from atmospheric concentration measurements at remote sites around the world. We find that global CFC-11 emissions decreased by 18 ± 6 gigagrams per year (26 ± 9 per cent; one standard deviation) from 2018 to 2019, to a 2019 value (52 ± 10 gigagrams per year) that is similar to the 2008-2012 mean. The decline in global emissions suggests a substantial decrease in unreported CFC-11 production. If the sharp decline in unexpected global emissions and unreported production is sustained, any associated future ozone depletion is likely to be limited, despite an increase in the CFC-11 bank (the amount of CFC-11 produced, but not yet emitted) by 90 to 725 gigagrams by the beginning of 2020.

Emissions of ozone-depleting substances, including trichlorofluoromethane (CFC-11), have decreased since the mid-1980s in response to the Montreal Protocol 1,2 . In recent years, an unexpected increase in CFC-11 emissions beginning in 2013 has been reported, with much of the global rise attributed to emissions from eastern China 3,4 . Here we use high-frequency atmospheric mole fraction observations from Gosan, South Korea and Hateruma, Japan, together with atmospheric chemical transport-model simulations, to investigate regional CFC-11 emissions from eastern China. We find that CFC-11 emissions returned to pre-2013 levels in 2019 (5.0 ± 1.0 gigagrams per year in 2019, compared to 7.2 ± 1.5 gigagrams per year for 2008-2012, ±1 standard deviation), decreasing by 10 ± 3 gigagrams per year since 2014-2017. Furthermore, we find that in this region, carbon tetrachloride (CCl 4 ) and dichlorodifluoromethane (CFC-12) emissions-potentially associated with CFC-11 production-were higher than expected after 2013 and then declined one to two years before the CFC-11 emissions reduction. This suggests that CFC-11 production occurred in eastern China after the mandated global phase-out, and that there was a subsequent decline in production during 2017-2018. We estimate that the amount of the CFC-11 bank (the amount of CFC-11 produced, but not yet emitted) in eastern China is up to 112 gigagrams larger in 2019 compared to pre-2013 levels, probably as a result of recent production. Nevertheless, it seems that any substantial delay in ozone-layer recovery has been avoided, perhaps owing to timely reporting 3,4 and subsequent action by industry and government in China 5,6 .

Unregulated chlorocarbons, here defined as dichloromethane (CH 2 Cl 2 ), perchloroethene (C 2 Cl 4 ), chloroform (CHCl 3 ), and methyl chloride (CH 3 Cl), are gases not regulated by the Montreal Protocol. While CH 3 Cl is the largest contributor of atmospheric chlorine, recent studies have shown that growth in emissions of the less abundant chlorocarbons could pose a significant threat to the recovery of the ozone layer. Despite this, there remain many regions for which no atmospheric monitoring exists, leaving gaps in our understanding of global emissions. Here, we report on a new time series of chlorocarbon measurements from Cape Point, South Africa for 2017, which represent the first published high-frequency measurements of these gases from Africa. For CH 2 Cl 2 and C 2 Cl 4 , the majority of mole fraction enhancements were observed from the north, consistent with anthropogenically modified air from Cape Town, while for CHCl 3 and CH 3 Cl, we found evidence for both oceanic and terrestrial sources. Using an inverse method, we estimated emissions for south-western South Africa (SWSA). For each chlorocarbon, SWSA accounted for less than 1% of global emissions. For CH 2 Cl 2 and C 2 Cl 4 , we extrapolated using population statistics and found South African emissions of 8.9 (7.4-10.4) Gg yr -1 and 0.80 (0.64-1.04) Gg yr -1 , respectively.

Cohesive particles in aquatic systems can play an important role in determining the fate of spilled oil via the generation of Oil-Mineral Aggregates (OMAs). Series of laboratory experiments have been conducted aiming at filling the knowledge gap regarding how cohesive clay particles influence the accumulation of petroleum through forming different aggregate structures and their resulting settling velocity. OMAs have been successfully created in a stirring jar with artificial sea-water, crude oil and two types of most common cohesive minerals, Kaolinite and Bentonite clay. With the magnetic stirrer adjusted to 490 rpm to provide a high level homogeneous flow turbulence (Turbulence dissipation ε estimated to be about 0.02 m 2 ⋅s -3 ), droplet OMAs and flake/solid OMAs were obtained in oil-Kaolinite sample and oil-Bentonite sample, respectively. Kaolinite clay with relatively low flocculation rate (R f  = 0.13 min -1 ) tends to physically attach around the surface of oil droplets. With the lower density of oil, these oil-Kaolinite droplet OMAs generally show lower settling velocity comparing to pure mineral Kaolinite flocs. Differently, Bentonite clay with higher flocculation rate (R f  = 0.66 min -1 ) produces more porous flocs that can absorb or be absorbed by the oil and form compact flake/solid OMAs with higher density and settling velocity than pure Bentonite flocs. In the mixed Kaolinite-Bentonite sample (1:1 in weight), oil is observed to preferably interacting with Bentonite and increase settling velocity especially in larger floc size classes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

This study was conducted to determine the effects of a co-infection with Moritella viscosa at different exposure levels of sea lice Lepeophtheirus salmonis in Atlantic salmon (Salmo salar). M. viscosa (1.14 × 10 6  cfu/ml) was introduced to all experimental tanks at 10 days post-lice infection (dpLs). Mean lice counts decreased over time in both the medium lice co-infection (31.5 ± 19.0 at 7 dpLs; 16.9 ± 9.3 at 46 dpLs) and high lice co-infection (62.0 ± 10.8 at 7 dpLs; 37.6 ± 11.3 at 46 dpLs). There were significantly higher mortalities and more severe skin lesions in the high lice co-infected group compared to medium lice co-infected group or M. viscosa-only infection. Quantitative gene expression analysis detected a significant upregulation of genes in skin from the high lice co-infection group consistent with severe inflammation (il-8, mmp-9, hep, saa). Skin lesions retrieved throughout the study were positive for M. viscosa growth, but these were rarely located in regions associated with lice. These results suggest that while M. viscosa infection itself may induce skin lesion development in salmon, co-infection with high numbers of lice can enhance this impact and significantly reduce the ability of these lesions to resolve, resulting in increased mortality., (© 2020 John Wiley & Sons Ltd.)

The shape and size of sedimentary bedforms play a key role in the reconstruction of sedimentary processes in modern and ancient environments. Recent laboratory experiments have shown that bedforms in mixed sand-clay develop at a slower rate and often have smaller heights and wavelengths than equivalent bedforms in pure sand. This effect is generally attributed to cohesive forces that can be of physical origin, caused by electrostatic forces of attraction between clay minerals, and of biological origin, caused by 'sticky' extracellular polymeric substances (EPS) produced by micro-organisms, such as microalgae (microphytobenthos) and bacteria. The present study demonstrates, for the first time, that these laboratory experiments are a suitable analogue for current ripples formed by tidal currents on a natural mixed sand-mud-EPS intertidal flat in a macrotidal estuary. Integrated hydrodynamic and bed morphological measurements, collected during a spring tide under weak wave conditions near Hilbre Island (Dee Estuary, north-west England, UK), reveal a statistically significant decrease in current ripple wavelength for progressively higher bed mud and EPS contents, and a concurrent change from three-dimensional linguoid to two-dimensional straight-crested ripple planform morphology. These results agree well with observations in laboratory flumes, but the rate of decrease of ripple wavelength as mud content increased was found to be substantially greater for the field than the laboratory. Since the formation of ripples under natural conditions is inherently more complex than in the laboratory, four additional factors that might affect current ripple development in estuaries, but which were not accounted for in laboratory experiments, were explored. These were current forcing, clay type, pore water salinity and bed EPS content. These data illustrate that clay type alone cannot explain the difference in the rate of decrease in ripple wavelength, because the bed clay contents were too low for clay type to have had a measurable effect on bedform development. Accounting for the difference in current forcing between the field and experiments, and therefore the relative stage of development with respect to equilibrium ripples, increases the difference between the ripple wavelengths. The presence of strongly cohesive EPS in the current ripples on the natural intertidal flat might explain the majority of the difference in the rate of decrease in ripple wavelength between the field and the laboratory. The effect of pore water salinity on the rate of bedform development cannot be quantified at present, but salinity is postulated herein to have had a smaller influence on the ripple wavelength than bed EPS content. The common presence of clay and EPS in many aqueous sedimentary environments implies that a re-assessment of the role of current ripples and their primary current lamination in predicting and reconstructing flow regimes is necessary, and that models that are valid for pure sand are an inappropriate descriptor for more complex mixed sediment. This study proposes that this re-assessment is necessary at all bed clay contents above 3%., (© 2019 The Authors. Sedimentology published by John Wiley © Sons Ltd on behalf of International Association of Sedimentologists.)

One hydrochlorofluorocarbon and two hydrofluorocarbons (HCFC-22, HFC-125, and HFC-152a) were measured in air samples at the Cape Point observatory (CPT), South Africa, during 2017. These data represent the first such atmospheric measurements of these compounds from southwestern South Africa (SWSA). Baseline atmospheric growth rates were estimated to be 8.36, 4.10, and 0.71 ppt year -1 for HCFC-22, HFC-125, and HFC-152a, respectively. The CPT measurements were combined with an inverse model to investigate emissions from SWSA. For all three halocarbons, Cape Town was found to be the dominant source within SWSA. These estimates were extrapolated, based on population statistics, to estimate emissions for the whole of South Africa. We estimate South Africa's 2017 emissions to be 3.0 (1.6-4.4), 0.8 (0.5-1.2), and 1.1 (0.6-1.6) Gg year -1 for HCFC-22, HFC-125, and HFC-152a, respectively. For all three halocarbons, South Africa's contribution to global emissions is small (<2.5%), but future monitoring is needed to ensure South Africa's compliance with regulation set out by the Montreal Protocol and its Amendments.

The recovery of the stratospheric ozone layer relies on the continued decline in the atmospheric concentrations of ozone-depleting gases such as chlorofluorocarbons 1 . The atmospheric concentration of trichlorofluoromethane (CFC-11), the second-most abundant chlorofluorocarbon, has declined substantially since the mid-1990s 2 . A recently reported slowdown in the decline of the atmospheric concentration of CFC-11 after 2012, however, suggests that global emissions have increased 3,4 . A concurrent increase in CFC-11 emissions from eastern Asia contributes to the global emission increase, but the location and magnitude of this regional source are unknown 3 . Here, using high-frequency atmospheric observations from Gosan, South Korea, and Hateruma, Japan, together with global monitoring data and atmospheric chemical transport model simulations, we investigate regional CFC-11 emissions from eastern Asia. We show that emissions from eastern mainland China are 7.0 ± 3.0 (±1 standard deviation) gigagrams per year higher in 2014-2017 than in 2008-2012, and that the increase in emissions arises primarily around the northeastern provinces of Shandong and Hebei. This increase accounts for a substantial fraction (at least 40 to 60 per cent) of the global rise in CFC-11 emissions. We find no evidence for a significant increase in CFC-11 emissions from any other eastern Asian countries or other regions of the world where there are available data for the detection of regional emissions. The attribution of any remaining fraction of the global CFC-11 emission rise to other regions is limited by the sparsity of long-term measurements of sufficient frequency near potentially emissive regions. Several considerations suggest that the increase in CFC-11 emissions from eastern mainland China is likely to be the result of new production and use, which is inconsistent with the Montreal Protocol agreement to phase out global chlorofluorocarbon production by 2010.

The problem of early sexual maturation among farmed Arctic charr and other salmonids can be effectively reduced by 24 h light overwinter, provided it is bright enough to over-ride interference from the natural daylength cycle. To determine the threshold light intensity to suppress the nocturnal elevation of plasma melatonin, three groups of individually tagged fish (n = 26-28/group ca. 1040 g) were reared on 12 h light: 12 h dark (LD 12:12) and subjected to nighttime light intensities of either 50-65, 0.1-0.3 or 0 (control) lux for five months (November to April). Daytime light intensity was 720-750 lx. Diel plasma melatonin profiles in both November and April were similar; mean daytime levels ranged from 20 to 100 pg/ml, and nighttime levels were inversely proportional to light intensity. In the control group at 0 lx, plasma melatonin increased about four-fold after lights-off, ranging between 320 and 430 pg/ml. Nighttime light intensity of 0.1-0.3 lx halved plasma melatonin levels to 140-220 pg/ml, and 50-65 lx further reduced the levels to one quarter of the control group, 68-108 pg/ml. Among the lit groups, daytime plasma melatonin levels were about 20-30 pg/ml, significantly lower than the nocturnal levels suggesting the diel hormonal rhythm was not completely abolished. Fish grew steadily from about 1100 g to 1600 g between November and April, independent of light intensity (P = .67). Overall, the study demonstrated the sensitivity of pineal melatonin hormone to different light intensities in Arctic charr., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Biofilm-sediment aggregate (BSA) contains a high water content, either within internal pores and channels or bound by extracellular polymeric substances (EPS) forming a highly hydrated biofilm matrix. Desiccation of BSAs alters the biofilm morphology and thus the physical characteristics of porous media, such as the binding matrix within BSA and internal pore geometry. Observing BSAs in their naturally hydrated form is essential but hampered due to the lack of techniques for imaging and discerning hydrated materials. Generally, imagery techniques (scanning electron microscopy (SEM), transmission electron microscopy (TEM), and focused ion beam nanotomography (FIB-nt)) involve the desiccation of BSAs (freeze-drying or acetone dehydration) or prevent differentiation between BSA components such as inorganic particles and pore water (confocal laser scanning microscopic (CLSM)). Here, we propose a novel methodology that simultaneously achieves the 3D visualization and quantification of BSAs and their components in their hydrated form at a submicron resolution using X-ray microcomputed tomography (μ-CT). It enables the high-resolution detection of comparable morphology of multiphase components within a hydrated aggregate: each single inorganic particle and the hydrated biofilm matrix. This allows the estimation of aggregate density and the illustration of biofilm-sediment binding matrix. This information provides valuable insights into investigations of the transport of BSAs and aggregate-associated sediment particles, contaminants (such as microplastics), organic carbon, and their impacts on aquatic biogeochemical cycling.

NF-κB is an important mediator of immune activity and its activation is essential in mounting immune response to pathogens. Here, we describe the optimization and implementation of a high-throughput screening platform that utilizes high content imaging and analysis to monitor NF-κB nuclear translocation. We screened 38,991 compounds from three different small molecule libraries and identified 103 compound as hits; 31% of these were active in a dose response assay. Several of the molecules lacked cytotoxicity or had a selectivity index of more than 2-fold. Our image-based approach provides an important first step towards identifying small molecules with immunomodulatory activity., Competing Interests: The authors have read the journal's policy and the authors of this manuscript have the following competing interests: TP is on the Editorial board for PLOS One. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

The Montreal Protocol was designed to protect the stratospheric ozone layer by enabling reductions in the abundance of ozone-depleting substances such as chlorofluorocarbons (CFCs) in the atmosphere 1-3 . The reduction in the atmospheric concentration of trichlorofluoromethane (CFC-11) has made the second-largest contribution to the decline in the total atmospheric concentration of ozone-depleting chlorine since the 1990s 1 . However, CFC-11 still contributes one-quarter of all chlorine reaching the stratosphere, and a timely recovery of the stratospheric ozone layer depends on a sustained decline in CFC-11 concentrations 1 . Here we show that the rate of decline of atmospheric CFC-11 concentrations observed at remote measurement sites was constant from 2002 to 2012, and then slowed by about 50 per cent after 2012. The observed slowdown in the decline of CFC-11 concentration was concurrent with a 50 per cent increase in the mean concentration difference observed between the Northern and Southern Hemispheres, and also with the emergence of strong correlations at the Mauna Loa Observatory between concentrations of CFC-11 and other chemicals associated with anthropogenic emissions. A simple model analysis of our findings suggests an increase in CFC-11 emissions of 13 ± 5 gigagrams per year (25 ± 13 per cent) since 2012, despite reported production being close to zero 4 since 2006. Our three-dimensional model simulations confirm the increase in CFC-11 emissions, but indicate that this increase may have been as much as 50 per cent smaller as a result of changes in stratospheric processes or dynamics. The increase in emission of CFC-11 appears unrelated to past production; this suggests unreported new production, which is inconsistent with the Montreal Protocol agreement to phase out global CFC production by 2010.

Enzyme-dependent post-translational modifications (PTMs) mediate the cellular regulation of proteins and can be discovered using proteomics. However, even where the peptides of interest can be enriched for analysis with state-of-the-art LC-MS/MS tools and informatics, only a fraction of peptide ions can be identified confidently. Thus, many PTM sites remain undiscovered and unconfirmed. In this minireview, we use a case study to discuss how the use of inclusion lists, turning off isotopic exclusion, and manual validation significantly increased depth of coverage, facilitating discovery of acetylation sites in targets of an acetyltransferase virulence factor. These underutilized strategies have the potential to help answer many mechanistic biological questions that large-scale proteomic studies cannot., (Copyright © 2017. Published by Elsevier B.V.)

Tuberculosis is one of the infectious diseases with the greatest global burden, affecting millions of people. The rise of multi- and extensively-drug resistant forms of Mycobacterium tuberculosis over the last few decades has highlighted the urgent need for development of new drugs to treat the disease. Many drug development pipelines are based on in vitro assays examining a compound's effect on M. tuberculosis alone. These do not account for the effect of a compound on mammalian cells nor the interaction between host and pathogen. We therefore developed a live-cell fluorescence-based screen utilizing high content microscopy of mammalian macrophages infected with M. tuberculosis to screen for compounds with both substantial inhibition of M. tuberculosis growth and low cytotoxicity. Isoniazid, a first line tuberculosis drug, and staurosporine, a compound with well documented cytotoxic activity, were used to validate the assay. These and other control compounds showed results for M. tuberculosis growth consistent with the field. Together, this method of screening allows for high throughput testing of potential tuberculosis drugs while capturing more information per compound in a physiologically relevant context., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)

The growth in global methane (CH 4 ) concentration, which had been ongoing since the industrial revolution, stalled around the year 2000 before resuming globally in 2007. We evaluate the role of the hydroxyl radical (OH), the major CH 4 sink, in the recent CH 4 growth. We also examine the influence of systematic uncertainties in OH concentrations on CH 4 emissions inferred from atmospheric observations. We use observations of 1,1,1-trichloroethane (CH 3 CCl 3 ), which is lost primarily through reaction with OH, to estimate OH levels as well as CH 3 CC 3 emissions, which have uncertainty that previously limited the accuracy of OH estimates. We find a 64-70% probability that a decline in OH has contributed to the post-2007 methane rise. Our median solution suggests that CH 4 emissions increased relatively steadily during the late 1990s and early 2000s, after which growth was more modest. This solution obviates the need for a sudden statistically significant change in total CH 4 emissions around the year 2007 to explain the atmospheric observations and can explain some of the decline in the atmospheric 13 CH 4 / 12 CH 4 ratio and the recent growth in C 2 H 6 Our approach indicates that significant OH-related uncertainties in the CH 4 budget remain, and we find that it is not possible to implicate, with a high degree of confidence, rapid global CH 4 emissions changes as the primary driver of recent trends when our inferred OH trends and these uncertainties are considered., Competing Interests: The authors declare no conflict of interest.

A stratified air mass enriched in methane (CH 4 ) was sampled at ~600 m to ~2000 m altitude, between the north coast of Norway and Svalbard as part of the Methane in the Arctic: Measurements and Modelling campaign on board the UK's BAe-146-301 Atmospheric Research Aircraft. The approach used here, which combines interpretation of multiple tracers with transport modeling, enables better understanding of the emission sources that contribute to the background mixing ratios of CH 4 in the Arctic. Importantly, it allows constraints to be placed on the location and isotopic bulk signature of the emission source(s). Measurements of δ 13 C in CH 4 in whole air samples taken while traversing the air mass identified that the source(s) had a strongly depleted bulk δ 13 C CH 4 isotopic signature of -70 (±2.1)‰. Combined Numerical Atmospheric-dispersion Modeling Environment and inventory analysis indicates that the air mass was recently in the planetary boundary layer over northwest Russia and the Barents Sea, with the likely dominant source of methane being from wetlands in that region.

Independent verification of national greenhouse gas inventories is a vital measure for cross-checking the accuracy of emissions data submitted to the United Nations Framework Convention on Climate Change (UNFCCC). We infer annual UK emissions of HFC-134a from 1995 to 2012 using atmospheric observations and an inverse modeling technique, and compare with the UK's annual UNFCCC submission. By 2010, the inventory is almost twice as large as our estimates, with an "emissions gap" equating to 3.90 (3.20-4.30) Tg CO 2 e. We evaluate the RAC (Refrigeration and Air-Conditioning) model, a bottom up model used to quantify UK emissions from refrigeration and air-conditioning sectors. Within mobile air-conditioning (MAC), the largest RAC sector and most significant UK source (59%), we find a number of assumptions that may be considered oversimplistic and conservative; most notably the unit refill rate. Finally, a Bayesian approach is used to estimate probable inventory inputs required for minimization of the emissions discrepancy. Our top-down estimates provide only a weak constraint on inventory model parameters and consequently, we are unable to suggest discrete values. However, a significant revision of the MAC servicing rate, coupled with a reassessment of non-RAC aerosol emissions, are required if the discrepancy between methods is to be reduced.

Biologically active, fine-grained sediment forms abundant sedimentary deposits on Earth's surface, and mixed mud-sand dominates many coasts, deltas, and estuaries. Our predictions of sediment transport and bed roughness in these environments presently rely on empirically based bed form predictors that are based exclusively on biologically inactive cohesionless silt, sand, and gravel. This approach underpins many paleoenvironmental reconstructions of sedimentary successions, which rely on analysis of cross-stratification and bounding surfaces produced by migrating bed forms. Here we present controlled laboratory experiments that identify and quantify the influence of physical and biological cohesion on equilibrium bed form morphology. The results show the profound influence of biological cohesion on bed form size and identify how cohesive bonding mechanisms in different sediment mixtures govern the relationships. The findings highlight that existing bed form predictors require reformulation for combined biophysical cohesive effects in order to improve morphodynamic model predictions and to enhance the interpretations of these environments in the geological record.

Modifications of plant immune complexes by secreted pathogen effectors can trigger strong immune responses mediated by the action of nucleotide binding-leucine-rich repeat immune receptors. Although some strains of the pathogen Pseudomonas syringae harbor effectors that individually can trigger immunity, the plant's response may be suppressed by other virulence factors. This work reveals a robust strategy for immune suppression mediated by HopZ3, an effector in the YopJ family of acetyltransferases. The suppressing HopZ3 effector binds to and can acetylate multiple members of the RPM1 immune complex, as well as two P. syringae effectors that together activate the RPM1 complex. These acetylations modify serine, threonine, lysine, and/or histidine residues in the targets. Through HopZ3-mediated acetylation, it is possible that the whole effector-immune complex is inactivated, leading to increased growth of the pathogen., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Very short-lived brominated substances (VSLBr) are an important source of stratospheric bromine, an effective ozone destruction catalyst. However, the accurate estimation of the organic and inorganic partitioning of bromine and the input to the stratosphere remains uncertain. Here, we report near-tropopause measurements of organic brominated substances found over the tropical Pacific during the NASA Airborne Tropical Tropopause Experiment campaigns. We combine aircraft observations and a chemistry-climate model to quantify the total bromine loading injected to the stratosphere. Surprisingly, despite differences in vertical transport between the Eastern and Western Pacific, VSLBr (organic + inorganic) contribute approximately similar amounts of bromine [∼6 (4-9) parts per trillion] [corrected] to the stratospheric input at the tropical tropopause. These levels of bromine cause substantial ozone depletion in the lower stratosphere, and any increases in future abundances (e.g., as a result of aquaculture) will lead to larger depletions.

The epithelial to mesenchymal transition (EMT) is an essential process that occurs repeatedly during embryogenesis whereby stably adherent cells convert to an actively migrating state. While much is known about the factors and events that initiate the EMT, the steps that cells undergo to become directionally migratory are far less well understood. Zebrafish embryos lacking the transcription factors Tbx16/Spadetail and Mesogenin1 (Msgn1) are a valuable system for investigating the EMT. Mesodermal cells in these embryos are unable to perform the EMT necessary to leave the most posterior end of the body (the tailbud) and join the pre-somitic mesoderm, a process that is conserved in all vertebrates. It has previously been very difficult to study this EMT in vertebrates because of the multiple cell types in the tailbud and the morphogenetic changes the whole embryo undergoes. Here, we describe a novel tissue explant system for imaging the mesodermal cell EMT in vivo that allows us to investigate the requirements for cells to acquire migratory properties during the EMT with high spatio-temporal resolution. This method revealed that, despite the inability of tbx16;msgn1-deficient cells to leave the tailbud, actin-based protrusions form surprisingly normally in these cells and they become highly motile. However, tbx16;msgn1-deficient cells have specific cell-autonomous defects in the persistence and anterior direction of migration because the lamellipodia they form are not productive in driving anteriorward migration. Additionally, we show that mesoderm morphogenesis and differentiation are separable and that there is a migratory cue that directs mesodermal cell migration that is independent of Tbx16 and Msgn1. This work defines changes that cells undergo as they complete the EMT and provides new insight into the mechanisms required in vivo for cells to become mesenchymal., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The production of outer membrane vesicles by Gram-negative bacteria has been well documented; however, the mechanism behind the biogenesis of these vesicles remains unclear. Here a high-throughput experimental method and systems-scale analysis was conducted to determine vesiculation values for the whole genome knockout library of Escherichia coli mutant strains (Keio collection). The resultant dataset quantitatively recapitulates previously observed phenotypes and implicates nearly 150 new genes in the process of vesiculation. Gene functional and biochemical pathway analyses suggest that mutations that truncate outer membrane structures such as lipopolysaccharide and enterobacterial common antigen lead to hypervesiculation, whereas mutants in oxidative stress response pathways result in lower levels. This study expands and refines the current knowledge regarding the cellular pathways required for outer membrane vesiculation in E. coli.

Anterior to posterior growth of the vertebrate body is fueled by a posteriorly located population of bipotential neuro-mesodermal progenitor cells. These progenitors have a limited rate of proliferation and their maintenance is crucial for completion of the anterior-posterior axis. How they leave the progenitor state and commit to differentiation is largely unknown, in part because widespread modulation of factors essential for this process causes organism-wide effects. Using a novel assay, we show that zebrafish Tbx16 (Spadetail) is capable of advancing mesodermal differentiation cell-autonomously. Tbx16 locks cells into the mesodermal state by not only activating downstream mesodermal genes, but also by repressing bipotential progenitor genes, in part through a direct repression of sox2. We demonstrate that tbx16 is activated as cells move from an intermediate Wnt environment to a high Wnt environment, and show that Wnt signaling activates the tbx16 promoter. Importantly, high-level Wnt signaling is able to accelerate mesodermal differentiation cell-autonomously, just as we observe with Tbx16. Finally, because our assay for mesodermal commitment is quantitative we are able to show that the acceleration of mesodermal differentiation is surprisingly incomplete, implicating a potential separation of cell movement and differentiation during this process. Together, our data suggest a model in which high levels of Wnt signaling induce a transition to mesoderm by directly activating tbx16, which in turn acts to irreversibly flip a bistable switch, leading to maintenance of the mesodermal fate and repression of the bipotential progenitor state, even as cells leave the initial high-Wnt environment., (© 2015. Published by The Company of Biologists Ltd.)

We infer global and regional emissions of five of the most abundant hydrofluorocarbons (HFCs) using atmospheric measurements from the Advanced Global Atmospheric Gases Experiment and the National Institute for Environmental Studies, Japan, networks. We find that the total CO2-equivalent emissions of the five HFCs from countries that are required to provide detailed, annual reports to the United Nations Framework Convention on Climate Change (UNFCCC) increased from 198 (175-221) Tg-CO2-eq ⋅ y(-1) in 2007 to 275 (246-304) Tg-CO2-eq ⋅ y(-1) in 2012. These global warming potential-weighted aggregated emissions agree well with those reported to the UNFCCC throughout this period and indicate that the gap between reported emissions and global HFC emissions derived from atmospheric trends is almost entirely due to emissions from nonreporting countries. However, our measurement-based estimates of individual HFC species suggest that emissions, from reporting countries, of the most abundant HFC, HFC-134a, were only 79% (63-95%) of the UNFCCC inventory total, while other HFC emissions were significantly greater than the reported values. These results suggest that there are inaccuracies in the reporting methods for individual HFCs, which appear to cancel when aggregated together.

Sediment fluxes in aquatic environments are crucially dependent on bedform dynamics. However, sediment-flux predictions rely almost completely on clean-sand studies, despite most environments being composed of mixtures of non-cohesive sands, physically cohesive muds and biologically cohesive extracellular polymeric substances (EPS) generated by microorganisms. EPS associated with surficial biofilms are known to stabilize sediment and increase erosion thresholds. Here we present experimental data showing that the pervasive distribution of low levels of EPS throughout the sediment, rather than the high surficial levels of EPS in biofilms, is the key control on bedform dynamics. The development time for bedforms increases by up to two orders of magnitude for extremely small quantities of pervasively distributed EPS. This effect is far stronger than for physical cohesion, because EPS inhibit sand grains from moving independently. The results highlight that present bedform predictors are overly simplistic, and the associated sediment transport processes require re-assessment for the influence of EPS.

Epithelia form the building blocks of many tissue and organ types. Epithelial cells often form a contiguous 2-dimensional sheet that is held together by strong adhesions. The mechanical properties conferred by these adhesions allow the cells to undergo dramatic three-dimensional morphogenetic movements while maintaining cell-cell contacts during embryogenesis and post-embryonic development. The Drosophila Folded gastrulation pathway triggers epithelial cell shape changes that drive gastrulation and tissue folding and is one of the most extensively studied examples of epithelial morphogenesis. This pathway has yielded key insights into the signaling mechanisms and cellular machinery involved in epithelial remodeling. In this review, we discuss principles of morphogenesis and signaling that have been discovered through genetic and cell biological examination of this pathway. We also consider various regulatory mechanisms and the system׳s relevance to mammalian development. We propose future directions that will continue to broaden our knowledge of morphogenesis across taxa., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)

Epithelial morphogenesis is essential for shaping organs and tissues and for establishment of the three embryonic germ layers during gastrulation. Studies of gastrulation in Drosophila have provided insight into how epithelial morphogenesis is governed by developmental patterning mechanisms. We developed an assay to recapitulate morphogenetic shape changes in individual cultured cells and used RNA interference-based screening to identify Mist, a Drosophila G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptor (GPCR) that transduces signals from the secreted ligand Folded gastrulation (Fog) in cultured cells. Mist functioned in Fog-dependent embryonic morphogenesis, and the transcription factor Snail regulated expression of mist in zygotes. Our data revealed how a cell fate transcriptional program acts through a ligand-GPCR pair to stimulate epithelial morphogenetic shape changes.