Accurate MS-based Rab10 Phosphorylation Stoichiometry Determination as Readout for LRRK2 Activity in Parkinson's Disease

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Highlights

• •MS-based clinical assay that accurately determines phospho Rab10 occupancy.
• •Stable isotope labeled phosphopeptide injected as a standard with endogenous tryptic phospho Rab peptide for accurate ratio determination.
• •Determination of pRab levels in neutrophils of Parkinson disease patients.
• •Relevance of pRab levels as marker of PD.

     

Enzymatic desulfurization of dibenzothiophene by a cell-free system of Rhodococcus erythropolis D-1

Abstract Pseudomonas syringae cells were exposed to Cu²⁺ alone or in the precence of acetate, proline or cysteine, at concentrations that reduced free Cu²⁺ to 1/10 of the total copper. Ligand concentrations (designated as isoeffective) were determined experimentally using a Cu²⁺-selective electrode and confirmed by computer calculations using published stability constants. Exposure of P. syringae cells to Cu²⁺ alone resulted in rapid and pronounced cell death, and binding of most of the copper in solution. The addition of acetate, proline or cysteine, a few minutes after Cu²⁺ treatment, resulted in a significant reduction in cell death, and in the amount of copper bound to the cells. For short exposures to Cu²⁺, cysteine was more effective than acetate or proline, but after 60 min of treatment, similar results were observed with these ligands. The addition of ligands before Cu²⁺ resulted in even more reduced copper toxicity. The results showed that, at isoeffective concentrations, weak and moderate copper-ligands can effectively antagonize copper toxicity, and that this protective effect does not require previously equilibrated copper-ligand solutions and is not very dependent of the nature of the ligand.     

Effect and design of buffer zones in the Nordic climate: The influence of width, amount of surface runoff, seasonal variation and vegetation type on retention efficiency for nutrient and particle runoff

Loss of nutrients and sediments from agricultural runoff causes eutrophication in surface water. Vegetated buffer zones adjacent to a stream can effectively remove and retain nutrients and sediments. It is, therefore, important to study design criteria which optimise the effect of buffer zones (BZ). This paper describes the influence of four criteria: (i) buffer zone width, (ii) amount of surface runoff water entering the BZ, (iii) seasonal variation and (iv) vegetation type. These parameters were studied after simulated and natural runoff at four different sites in Southern Norway with cold temperate climate. Surface runoff was collected before entering and after passing the BZs. The simulation experiments were short-term experiments carried out over a few days in 1992 and 1993. In the natural runoff experiments, volume proportional mixed samples were collected after each runoff period during 1992–1999. The results show significantly higher removal efficiency (in %) from 10 m wide BZs compared to 5 m widths, however, the specific retention (per m²) is higher in 5 m BZ. Buffer zones can receive particle runoff over several days without a significant decrease in their removal level. Retention efficiency between summer and autumn varied depending on the measured parameter (phosphorus, particles and nitrogen), and there were no significant differences in removal efficiency between summer and winter. The results show no significant differences between forest buffer zones (FBZ) and grass buffer zones (GBZ) regarding their retention efficiency for nitrogen and phosphorus. There was significantly higher retention efficiency in FBZ for particles. Average removal efficiencies from both simulated and natural runoff experiments varied from 60–89%, 37–81% and 81–91% for phosphorus, nitrogen and particles, respectively.     

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

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Highlights

• •Higher AGC significantly improves quantitation quality in single-cell analysis.
• •The boosting-to-sample ratio should be carefully evaluated and optimized.
• •iBASIL allows for precise quantitation of 1,500 proteins from 104 AML single cells.
• •iBASIL recapitulates major biological differences in different AML single cells.

     

Does rock chemistry affect periphyton accrual in streams?

Stones of different rock types often accrue different amounts of periphytic algae. Although algal biomass may be positively related to stone roughness, the confounding role of rock chemistry is unclear. This independent effect of rock chemistry on benthic algae was tested using the nutrient-diffusing technique, by incorporating powdered stone, rather than nutrients, into the agar matrix. Rocks tested were sandstone, obsidian, schist, greywacke, pumice, gypsum, limestone, serpentine, and phosphorite. Petri-dishes containing powdered rock and agar, and covered with a permeable cellulose filter, were incubated in eight pools in a granitic stream. Algal biomass did not differ among any of the nine rock types and plain agar control, whereas biomass differed among the concurrently placed nutrient diffusing substrates (the stream was phosphorus-limited). Algal composition was more related to an upstream-downstream gradient (for filamentous algae) and pool-specific effects (deposition of fine sediment for diatoms) than rock chemistry. This minimal effect of rock chemistry may be caused by the low dissolution rate of stones. Handling editor: J. Padisak     

Cobalt-dependent transcription of the nitrile hydratase gene in Rhodococcus rhodochrous M8

Abstract The effects of cobalt ions on the activities of Rhodococcus rhodochrous M8 enzymes for nitrile utilization, nitrile hydratase and amidase, were investigated. In contrast to amidase, synthesis of nitrile hydratase and its activity required cobalt ions in the growth medium. Northern blot analysis showed that in the presence of cobalt ions, the level of mRNA for nitrile hydratase genes was several times higher than that under cobalt-limited conditions. It was assumed that the low nitrile hydratase activity in cells grown in the absence of cobalt ions is connected either with the weak expression of nitrile hydratase genes or with the rapid degradation of nitrile hydratase mRNA.     

Development of an epiphyte indicator of nutrient enrichment: A critical evaluation of observational and experimental studies

An extensive review of the literature describing epiphytes on submerged aquatic vegetation (SAV), especially seagrasses, was conducted in order to evaluate the evidence for response of epiphyte metrics to increased nutrients. Evidence from field observational studies, together with laboratory and field mesocosm experiments, was assembled from the literature and evaluated for a hypothesized positive response to nutrient addition. There was general consistency in the results to confirm that elevated nutrients tended to increase the load of epiphytes on the surface of SAV, in the absence of other limiting factors. In spite of multiple sources of uncontrolled variation, positive relationships of epiphyte load to nutrient concentration or load (either nitrogen or phosphorus) often were observed along strong anthropogenic or natural nutrient gradients in coastal regions. Such response patterns may only be evident for parts of the year. Results from both mesocosm and field experiments also generally support the increase of epiphytes with increased nutrients, although outcomes from field experiments tended to be more variable. Relatively few studies with nutrient addition in mesocosms have been done with tropical or subtropical species, and more such controlled experiments would be helpful. Experimental duration influenced results, with more positive responses of epiphytes to nutrients at shorter durations in mesocosm experiments versus more positive responses at longer durations in field experiments. In the field, response of epiphyte biomass to nutrient additions was independent of climate zone. Mesograzer activity was a critical covariate for epiphyte response under experimental nutrient elevation, but the epiphyte response was highly dependent on factors such as grazer identity and density, as well as nutrient and ambient light levels. The balance of evidence suggests that epiphytes on SAV will be a useful indicator of persistent nutrient enhancement in many situations. Careful selection of appropriate temporal and spatial constraints for data collection, and concurrent evaluation of confounding factors will help increase the signal to noise ratio for this indicator.     

Historical record of human impact in a lake of northern China: Magnetic susceptibility,nutrients, heavy metals and OCPs

The historical record (1859–2011) of magnetic susceptibility, total organic carbon, total nitrogen, δ¹³C_org, δ¹⁵N, As, Cd, Hg, Pb, and organochlorine pesticide (OCP) signatures in Baiyangdian Lake was used to analyze the water environmental changes due to human activities. The results indicate the following: the status of the lake approaches the background condition in 1859–1950s; the lake suffered increasing anthropogenic effects from the 1950s because of increasing human activities such as coal-fired power plant operations since 1958, fertilizer use in the agriculture and land transformation since the 1950s, steelmaking between the 1960s and 1970s, machinery manufacturing since the 1970s, use of petrol containing alky-lead since 1990; the lake has been in a contaminated condition since the 2000s. This study confirms that OCPs have been effectively controlled in the area, the level of nutrient and heavy metal pollution is increasing, coal-fired power plants are an important source of Hg, and the use of petrol containing alky-lead has accelerated the accumulation of Pb in the environment. The study indicates that magnetic susceptibility can be used as a rapid, simple, and non-destructive tool for assessment of organic and heavy metal pollution in the lake.     

Intracellular water volume and internal pH of Streptomyces antibioticus spores

Abstract In the present study we compared the intracellular level of free calcium ([Ca²⁺]_i) and monomeric (G)/total (G + F) actin ratio in HeLa cells infected with diffuse (DAEC) and localised adherent Escherichia coli (LAEC). The level of [Ca²⁺]_i was increased in both DAEC- and LAEC-infected HeLa cells. However, studies with EGTA- and dantrolene-treated cells and also suspension of cells in Ca²⁺-free buffer suggested that the rise of [Ca²⁺]_i in DAEC-infected cells was due to the influx of Ca²⁺ from extracellular medium, whereas Ca²⁺ mobilisation from the intracellular stores was responsible for the enhancement of [Ca²⁺]_i in LAEC-infected cells. It was also evident that the infection of HeLa cells with DAEC and LAEC caused alteration of G / G + F actin ratio as compared to that of control cells. The ratio was much lower in LAEC-infected cells than that of DAEC-infected ones. Moreover, cytochalasin B inhibited both DAEC and LAEC invasion to HeLa cells, suggesting further the role of microfilaments in the invasion process.