Pseudomonas syringae effector HopZ3 suppresses the bacterial AvrPto1-tomato PTO immune complex via acetylation.

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.

On the role of organic matter composition in fresh-water kaolinite flocculation.

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 (Np) 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 Np and Dm and found that larger Np 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.

Burst or Conventional Peripheral Nerve Field Stimulation for Treatment of Neuropathic Facial Pain.

BACKGROUND: Trigeminal Neuropathic Pain (TNP) is a chronic facial pain syndrome caused by a lesion or disease affecting one or more branches of the trigeminal nerve. It may, for example, result from accidental injury to a branch of the trigeminal nerve by trauma or during surgery; it may also be idiopathic. TNP is typically constant, in contrast to most cases of the commoner trigeminal neuralgia. In some cases, pain may be refractory to pharmacological treatment. Peripheral nerve field stimulation is recognized as an effective minimally invasive surgical treatment option for this debilitating condition. To date, stimulation has used conventional tonic waveforms, which generate paraesthesia in the stimulated area. This is the first report of the use of paraesthesia-free burst pattern stimulation for TNP. METHODS: Seven patients were treated at the John Radcliffe Hospital for TNP from 2016 to 2018. Mean duration of preoperative symptoms was five years. All patients had exhausted pharmacological measures to limited effect. The initial three patients had tonic stimulation with the subsequent four having burst stimulation. Outcome was assessed using the numeric pain rating scale preoperatively and postoperatively at three and six months and one year. Side-effects and complications were also assessed as well as reduction in analgesic medication use. RESULTS: All patients achieved pain reduction of at least 50% at 6 months (range 50-100%, mean 81%, p = 0.0082). Those in the burst stimulation group were paraesthesia free. One patient developed a postoperative infection for which the system had to be removed and is awaiting reimplantation. There were no other complications in either group. CONCLUSION: Burst stimulation conferred similar pain control to tonic stimulation in our small cohort, and there were similar reductions in pain medication use. An additional benefit of burst stimulation is freedom from paraesthesia. Larger scale studies are needed to further evaluate burst stimulation and compare its efficacy with that of tonic stimulation.

Integrating field and laboratory approaches for ripple development in mixed sand-clay-EPS.

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%.

Simple strategies to enhance discovery of acetylation post-translational modifications by quadrupole-orbitrap LC-MS/MS.

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.

Nondestructive 3D Imaging and Quantification of Hydrated Biofilm-Sediment Aggregates Using X-ray Microcomputed Tomography.

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.

The role of biophysical cohesion on subaqueous bed form size.

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.

Persistent reshaping of cohesive sediment towards stable flocs by turbulence.

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.

On the importance of temporal floc size statistics and yield strength for population balance equation flocculation model.

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 d50, 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 d16, d50 and d84, 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.

Climate-change-driven deterioration of water quality in a mineralized watershed.

A unique 30-year streamwater chemistry data set from a mineralized alpine watershed with naturally acidic, metal-rich water displays dissolved concentrations of Zn and other metals of ecological concern increasing by 100-400% (400-2000 µg/L) during low-flow months, when metal concentrations are highest. SO(4) and other major ions show similar increases. A lack of natural or anthropogenic land disturbances in the watershed during the study period suggests that climate change is the underlying cause. Local mean annual and mean summer air temperatures have increased at a rate of 0.2-1.2 °C/decade since the 1980s. Other climatic and hydrologic indices, including stream discharge during low-flow months, do not display statistically significant trends. Consideration of potential specific causal mechanisms driven by rising temperatures suggests that melting of permafrost and falling water tables (from decreased recharge) are probable explanations for the increasing concentrations. The prospect of future widespread increases in dissolved solutes from mineralized watersheds is concerning given likely negative impacts on downstream ecosystems and water resources, and complications created for the establishment of attainable remediation objectives at mine sites.

Novel quantification of regional fossil fuel CO2 reductions during COVID-19 lockdowns using atmospheric oxygen measurements.

It is not currently possible to quantify regional-scale fossil fuel carbon dioxide (ffCO2) emissions with high accuracy in near real time. Existing atmospheric methods for separating ffCO2 from large natural carbon dioxide variations are constrained by sampling limitations, so that estimates of regional changes in ffCO2 emissions, such as those occurring in response to coronavirus disease 2019 (COVID-19) lockdowns, rely on indirect activity data. We present a method for quantifying regional signals of ffCO2 based on continuous atmospheric measurements of oxygen and carbon dioxide combined into the tracer "atmospheric potential oxygen" (APO). We detect and quantify ffCO2 reductions during 2020-2021 caused by the two U.K. COVID-19 lockdowns individually using APO data from Weybourne Atmospheric Observatory in the United Kingdom and a machine learning algorithm. Our APO-based assessment has near-real-time potential and provides high-frequency information that is in good agreement with the spread of ffCO2 emissions reductions from three independent lower-frequency U.K. estimates.

Contribution of bacterial outer membrane vesicles to innate bacterial defense.

BACKGROUND: Outer membrane vesicles (OMVs) are constitutively produced by Gram-negative bacteria throughout growth and have proposed roles in virulence, inflammation, and the response to envelope stress. Here we investigate outer membrane vesiculation as a bacterial mechanism for immediate short-term protection against outer membrane acting stressors. Antimicrobial peptides as well as bacteriophage were used to examine the effectiveness of OMV protection. RESULTS: We found that a hyper-vesiculating mutant of Escherichia coli survived treatment by antimicrobial peptides (AMPs) polymyxin B and colistin better than the wild-type. Supplementation of E. coli cultures with purified outer membrane vesicles provided substantial protection against AMPs, and AMPs significantly induced vesiculation. Vesicle-mediated protection and induction of vesiculation were also observed for a human pathogen, enterotoxigenic E. coli (ETEC), challenged with polymyxin B. When ETEC with was incubated with low concentrations of vesicles concomitant with polymyxin B treatment, bacterial survival increased immediately, and the culture gained resistance to polymyxin B. By contrast, high levels of vesicles also provided immediate protection but prevented acquisition of resistance. Co-incubation of T4 bacteriophage and OMVs showed fast, irreversible binding. The efficiency of T4 infection was significantly reduced by the formation of complexes with the OMVs. CONCLUSIONS: These data reveal a role for OMVs in contributing to innate bacterial defense by adsorption of antimicrobial peptides and bacteriophage. Given the increase in vesiculation in response to the antimicrobial peptides, and loss in efficiency of infection with the T4-OMV complex, we conclude that OMV production may be an important factor in neutralizing environmental agents that target the outer membrane of Gram-negative bacteria.

A structure-function based approach to floc hierarchy and evidence for the non-fractal nature of natural sediment flocs.

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.

Cortical spreading ischaemia is a novel process involved in ischaemic damage in patients with aneurysmal subarachnoid haemorrhage.

The term cortical spreading depolarization (CSD) describes a wave of mass neuronal depolarization associated with net influx of cations and water. Clusters of prolonged CSDs were measured time-locked to progressive ischaemic damage in human cortex. CSD induces tone alterations in resistance vessels, causing either transient hyperperfusion (physiological haemodynamic response) in healthy tissue; or hypoperfusion [inverse haemodynamic response = cortical spreading ischaemia (CSI)] in tissue at risk for progressive damage, which has so far only been shown experimentally. Here, we performed a prospective, multicentre study in 13 patients with aneurysmal subarachnoid haemorrhage, using novel subdural opto-electrode technology for simultaneous laser-Doppler flowmetry (LDF) and direct current-electrocorticography, combined with measurements of tissue partial pressure of oxygen (ptiO(2)). Regional cerebral blood flow and electrocorticography were simultaneously recorded in 417 CSDs. Isolated CSDs occurred in 12 patients and were associated with either physiological, absent or inverse haemodynamic responses. Whereas the physiological haemodynamic response caused tissue hyperoxia, the inverse response led to tissue hypoxia. Clusters of prolonged CSDs were measured in five patients in close proximity to structural brain damage as assessed by neuroimaging. Clusters were associated with CSD-induced spreading hypoperfusions, which were significantly longer in duration (up to 144 min) than those of isolated CSDs. Thus, oxygen depletion caused by the inverse haemodynamic response may contribute to the establishment of clusters of prolonged CSDs and lesion progression. Combined electrocorticography and perfusion monitoring also revealed a characteristic vascular signature that might be used for non-invasive detection of CSD. Low-frequency vascular fluctuations (LF-VF) (f < 0.1 Hz), detectable by functional imaging methods, are determined by the brain's resting neuronal activity. CSD provides a depolarization block of the resting activity, recorded electrophysiologically as spreading depression of high-frequency-electrocorticography activity. Accordingly, we observed a spreading suppression of LF-VF, which accompanied spreading depression of high-frequency-electrocorticography activity, independently of whether CSD was associated with a physiological, absent or inverse haemodynamic response. Spreading suppressions of LF-VF thus allow the differentiation of progressive ischaemia and repair phases in a fashion similar to that shown previously for spreading depressions of high-frequency-electrocorticography activity. In conclusion, it is suggested that (i) CSI is a novel human disease mechanism associated with lesion development and a potential target for therapeutic intervention in stroke; and that (ii) prolonged spreading suppressions of LF-VF are a novel 'functional marker' for progressive ischaemia.

Oil-mineral flocculation and settling velocity in saline water.

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 m2⋅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 (Rf = 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 (Rf = 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.

Measurement and modelling of deep sea sediment plumes and implications for deep sea mining.

Deep sea mining concerns the extraction of poly-metallic nodules, cobalt-rich crusts and sulphide deposits from the ocean floor. The exploitation of these resources will result in adverse ecological effects arising from the direct removal of the substrate and, potentially, from the formation of sediment plumes that could result in deposition of fine sediment on sensitive species or entrainment of sediment, chemicals and nutrients into over-lying waters. Hence, identifying the behaviour of deep-sea sediment plumes is important in designing mining operations that are ecologically acceptable. Here, we present the results of novel in situ deep sea plume experiments undertaken on the Tropic seamount, 300 nautical miles SSW of the Canary Islands. These plume experiments were accompanied by hydrographic and oceanographic field surveys and supported by detailed numerical modelling and high resolution video settling velocity measurements of the in situ sediment undertaken in the laboratory. The plume experiments involved the controlled formation of benthic sediment plumes and measurement of the plume sediment concentration at a specially designed lander placed at set distances from the plume origin. The experiments were used as the basis for validation of a numerical dispersion model, which was then used to predict the dispersion of plumes generated by full-scale mining. The results highlight that the extent of dispersion of benthic sediment plumes, resulting from mining operations, is significantly reduced by the effects of flocculation, background turbidity and internal tides. These considerations must be taken into account when evaluating the impact and extent of benthic sediment plumes.

Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family.

Tyrosine ammonia-lyase (TAL) is a recently described member of the aromatic amino acid lyase family, which also includes phenylalanine (PAL) and histidine ammonia-lyases (HAL). TAL is highly selective for L-tyrosine, and synthesizes 4-coumaric acid as a protein cofactor or antibiotic precursor in microorganisms. In this report, we identify a single active site residue important for substrate selection in this enzyme family. Replacing the active site residue His89 with Phe in TAL completely switched its substrate selectivity from tyrosine to phenylalanine, thereby converting it into a highly active PAL. When a corresponding mutation was made in PAL, the enzyme lost PAL activity and gained TAL activity. The discovered substrate selectivity switch is a rare example of a complete alteration of substrate specificity by a single point mutation. We also show that the identity of the amino acid at the switch position can serve as a guide to predict substrate specificities of annotated aromatic amino acid lyases in genome sequences.

3H/3He age data in assessing the susceptibility of wells to contamination.

Regulatory agencies are becoming increasingly interested in using young-ground water dating techniques, such as the 3H/3He method, in assessing the susceptibility of public supply wells (PSWs) to contamination. However, recent studies emphasize that ground water samples of mixed age may be the norm, particularly from long-screened PSWs, and tracer-based "apparent" ages can differ substantially from actual mean ages for mixed-age samples. We present age and contaminant data from PSWs in Salt Lake Valley, Utah, that demonstrate the utility of 3H and 3He measurements in evaluating well susceptibility, despite potential age mixing. Initial 3H concentrations (measured 3H + measured tritiogenic 3He) are compared to those expected based on the apparent 3H/3He age and the local precipitation 3H record. This comparison is used to determine the amount of modern water (recharged after approximately 1950) vs. prebomb water (recharged before approximately 1950) samples might contain. Concentrations of common contaminants were also measured using detection limits generally lower than those used for regulatory purposes. A clear correlation exists between the potential magnitude of the modern water fraction and both the occurrence and concentration of contaminants. For samples containing dominantly modern water based on their initial 3H concentrations, potential discrepancies between apparent 3H/3He ages and mean ages are explored using synthetic samples that are random mixtures of different modern waters. Apparent ages can exceed mean ages by up to 13 years for these samples, with an exponential age distribution resulting in the greatest discrepancies.

Acetylation of an NB-LRR Plant Immune-Effector Complex Suppresses Immunity.

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.

Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli.

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.