Unveiling the components of the signaling pathway between endosomes and the phagocytic uptake machinery in Dictyostelium discoideum

The soil amoebae Dictyostelium discoideum take up particles from their environment in order to obtain nutrition. The particle transits through the cell within a phagosome that fuses with organelles of different molecular compositions, undergoing a gradual degradation by different sets of hydrolytic enzymes. Griffiths’ concept of “phagosome individuality” predicts signaling from phagosomes into the cytoplasm, which might regulate many aspects of cell physiology. The finding that Dictyostelium cells depleted of the lysozyme AlyA or over-expressing the esterase Gp70 exhibit increased uptake of food particles, led to the postulation of a signaling cascade between endocytic compartments and the cytoskeletal uptake machinery at the plasma membrane. Assuming that Gp70 acts downstream of AlyA, gene-expression profiling of both mutants revealed different and overlapping sets of misregulated genes that might participate in this signaling cascade. Based on these results, we analyzed the effects of the artificial misregulation of six candidate genes by over-expression or negative genetic interference, in order to reconstruct at least part of the signaling pathway. SSB420 and SSL793 were chosen as candidates for the first signaling step, as they were up-regulated in AlyA-null cells and remained unaltered in the Gp70 over-expressing cells. The over-expression of SSB420 enhanced phagocytosis and raised the expression levels of Gp70, supporting its involvement in the signaling pathway between AlyA and Gp70 as a positive regulator of phagocytosis. However, this was not the case of cells over-expressing SSL793, as this mutation had no effects on phagocytosis. For the signaling downstream of Gp70, we studied four commonly misregulated genes in AlyA-depleted and Gp70 over-expressing cells. The expression levels of SLB350, SSB389 and TipD were lower in both mutants and therefore these were assumed as possible candidates for the negative regulation of phagocytosis. Cells depleted of SLB350 exhibited an increased phagocytic activity and no effect on Gp70 expression, proving its participation in the signaling pathway downstream of Gp70. Unlike SLB350, the disruption of the genes coding for SSB389 and TipD had no effects on particle uptake, excluding them from the pathway. The fourth candidate was Yipf1, the only gene that was commonly up-regulated in both mutants. Yet, the artificial over-expression of this protein had no effects on phagocytosis, so this candidate is also not included in the signaling pathway. Furthermore, localizing the products of the candidate genes within the cell helped unveiling several cellular organelles that receive signals from the phagosome and transduce them towards the uptake machinery.

Ideotyping integrated aquaculture systems to balance soil nutrients

Due to growing land scarcity and lack of nutrient inputs, African farmers switched from shifting cultivation to continuous cropping and extended crop area by bringing fragile lands such as river banks and hill slopes into production. This accelerated soil fertility decline caused by erosion, harvesting and insufficient nutrient replenishment. We explored the feasibility to reduce nutrient depletion by increasing nutrient utilization efficiencies, while diversifying and increasing food production through the development of integrated aquaculture – agriculture (IAA). Considering the climatic conditions prevailing in Kenyan highlands, aquaculture production scenarios were ideotyped per agro-ecological zone. These aquaculture production scenarios were integrated into existing NUTrient MONitoring (NUTMON) farm survey data for the area. The nutrient balances and flows of the resulting IAA-systems were compared to present land use. The effects of IAA development on nutrient depletion and total food production were evaluated. With the development of IAA systems, nutrient depletion rates dropped by 23–35%, agricultural production increased by 2–26% and overall farm food production increased by 22–70%. The study demonstrates that from a bio-physical point of view, the development of IAA-systems in Africa is technically possible and could raise soil fertility and total farm production. Further studies that evaluate the economic feasibility and impacts on the livelihood of farming households are recommended.

Effect of environmental conditions on the N uptake route of soil microorganisms and adaption of a method to determine amino acid oxidase in soil

Soil microorganisms have evolved two possible mechanisms for their uptake of organic N: the direct route and the mobilization-immobilization-turnover (MIT) route. In the direct route, simple organic molecules are taken up via various mechanisms directly into the cell. In the MIT route, the deamination occurs outside the cell and all N is mineralized to NH4+ before assimilation. A better understanding of the mechanisms controlling the different uptake routes of soil microorganisms under different environmental conditions is crucial for understanding mineralization processes of organic material in soil. For the first experiment we incubated soil samples from the long term trial in Bad Lauchstädt with corn residues with different C to N ratios and inorganic N for 21 days at 20 °C. Under the assumption that all added amino acids were taken up or mineralized, the direct uptake route was more important in soil amended with corn residues with a wide C to N ratio. After 21 days of incubation the direct uptake of added amino acids increased in the order addition of corn residue with a: “C to N ratio of 40 & (NH4)2SO4 and no addition (control)” (69% and 68%, respectively) < “C to N ratio of 20” (73%) < “C to N ratio of 40” (95%). In all treatments the proportion of the added amino acids that were mineralized increased with time, indicating that the MIT route became more important over time. To investigate the effects of soil depth on the N uptake route of soil microorganisms (experiment II), soil samples in two soil depths (0-5 cm; 30-40 cm) were incubated with corn residues with different C to N ratios and inorganic N for 21 days at 20 °C and 60% (WHC). The addition of corn residue resulted in a marked increase of protease activity in both depths due to the induction from the added substrate. Addition of corn residue with a wide C to N ratio resulted in a significantly greater part of the direct uptake (97% and 94%) than without the addition of residues (85% and 80%) or addition of residue with a small C to N ratio (90% and 84%) or inorganic N (91% and 79% in the surface soil and subsoil, respectively), suggesting that under conditions of sufficient mineralizable N (C to N ratio of 20) or increased concentrations of NH4+, the enzyme system involved in the direct uptake is slightly repressed. Substrate additions resulted in an initially significantly higher increase of the direct uptake in the surface soil than in the subsoil. As a large proportion of the organic N input into soil is in form of proteinaceous material, the deamination of amino acids is a key reaction of the MIT route. Therefore the enzyme amino acid oxidase contribute to the extracellular N mineralization in soil. The objective of experiment III was to adapt a method to determine amino acid oxidase in soil. The detection via synthetic fluorescent Lucifer Yellow derivatives of the amino acid lysine is possible in soil. However, it was not possible to find the substrate concentration at which the reaction rate is independent of substrate concentration and therefore we were not able to develop a valid soil enzyme assay.

SBR technology for wastewater treatment: suitable operational conditions for a nutrient removal

Actualment, la legislació ambiental ha esdevingut més restrictiva pel que fa a la descàrrega d'aigües residuals amb nutrients, especialment en les anomenades àrees sensibles o zones vulnerables. Arran d'aquest fet, s'ha estimulat el coneixement, desenvolupament i millora dels processos d'eliminació de nutrients. El Reactor Discontinu Seqüencial (RDS) o Sequencing Batch Reactor (SBR) en anglès, és un sistema de tractament de fangs actius que opera mitjançant un procediment d'omplerta-buidat. En aquest tipus de reactors, l'aigua residual és addicionada en un sol reactor que treballa per càrregues repetint un cicle (seqüència) al llarg del temps. Una de les característiques dels SBR és que totes les diferents operacions (omplerta, reacció, sedimentació i buidat) es donen en un mateix reactor. La tecnologia SBR no és nova d'ara. El fet, és que va aparèixer abans que els sistema de tractament continu de fangs actius. El precursor dels SBR va ser un sistema d'omplerta-buidat que operava en discontinu. Entre els anys 1914 i 1920, varen sorgir certes dificultats moltes d'elles a nivell d'operació (vàlvules, canvis el cabal d'un reactor a un altre, elevat temps d'atenció per l'operari...) per aquests reactors. Però no va ser fins a finals de la dècada dels '50 principis del '60, amb el desenvolupament de nous equipaments i noves tecnologies, quan va tornar a ressorgir l'interès pels SBRs. Importants millores en el camp del subministrament d'aire (vàlvules motoritzades o d'acció pneumàtica) i en el de control (sondes de nivell, mesuradors de cabal, temporitzadors automàtics, microprocessadors) han permès que avui en dia els SBRs competeixin amb els sistemes convencional de fangs actius. L'objectiu de la present tesi és la identificació de les condicions d'operació adequades per un cicle segons el tipus d'aigua residual a l'entrada, les necessitats del tractament i la qualitat desitjada de la sortida utilitzant la tecnologia SBR. Aquestes tres característiques, l'aigua a tractar, les necessitats del tractament i la qualitat final desitjada determinen en gran mesura el tractament a realitzar. Així doncs, per tal d'adequar el tractament a cada tipus d'aigua residual i les seves necessitats, han estat estudiats diferents estratègies d'alimentació. El seguiment del procés es realitza mitjançant mesures on-line de pH, OD i RedOx, els canvis de les quals donen informació sobre l'estat del procés. Alhora un altre paràmetre que es pot calcular a partir de l'oxigen dissolt és la OUR que és una dada complementària als paràmetres esmentats. S'han avaluat les condicions d'operació per eliminar nitrogen d'una aigua residual sintètica utilitzant una estratègia d'alimentació esglaonada, a través de l'estudi de l'efecte del nombre d'alimentacions, la definició de la llargada i el número de fases per cicle, i la identificació dels punts crítics seguint les sondes de pH, OD i RedOx. S'ha aplicat l'estratègia d'alimentació esglaonada a dues aigües residuals diferents: una procedent d'una indústria tèxtil i l'altra, dels lixiviats d'un abocador. En ambdues aigües residuals es va estudiar l'eficiència del procés a partir de les condicions d'operació i de la velocitat del consum d'oxigen. Mentre que en l'aigua residual tèxtil el principal objectiu era eliminar matèria orgànica, en l'aigua procedent dels lixiviats d'abocador era eliminar matèria orgànica i nitrogen. S'han avaluat les condicions d'operació per eliminar nitrogen i fòsfor d'una aigua residual urbana utilitzant una estratègia d'alimentació esglaonada, a través de la definició del número i la llargada de les fases per cicle, i la identificació dels punts crítics seguint les sondes de pH, OD i RedOx. S'ha analitzat la influència del pH i la font de carboni per tal d'eliminar fòsfor d'una aigua sintètica a partir de l'estudi de l'increment de pH a dos reactors amb diferents fonts de carboni i l'estudi de l'efecte de canviar la font de carboni. Tal i com es pot veure al llarg de la tesi, on s'han tractat diferents aigües residuals per a diferents necessitats, un dels avantatges més importants d'un SBR és la seva flexibilitat.

Reduction of arsenic uptake by lettuce with ferrous sulfate applied to contaminated soil

Soil contamination by arsenic (As) presents a hazard in many countries and there is a need for techniques to minimize As uptake by plants. A proposed in situ remediation method was tested by growing lettuce (Lactuca sativa L. cv. Kermit) in a greenhouse pot experiment on soil that contained 577 mg As kg(-1), taken from a former As smelter site. All combinations of iron (Fe) oxides, at concentrations of 0.00, 0.22, 0.54, and 1.09% (w/w), and lime, at concentrations of 0.00, 0.27, 0.68, and 1.36% (w/w), were tested in a factorial design. To create the treatments, field-moist soil, commercial-grade FeSO4, and ground agricultural lime were mixed and stored for one week, allowing Fe oxides to precipitate. Iron oxides gave highly significant (P < 0.001) reductions in lettuce As concentrations, down to 11% of the lettuce As concentration for untreated soil. For the Fe oxides and lime treatment combinations where soil pH was maintained nearly constant, the lettuce As concentration declined in an exponential relationship with increasing FeSO4 application rate and lettuce yield was almost unchanged. Iron oxides applied at a concentration of 1.09% did not give significantly lower lettuce As concentrations than the 0.54% treatment. Simultaneous addition of lime with FeSO4 was essential. Ferrous sulfate with insufficient lime lowered soil pH and caused mobilization of Al, Ba, Co, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Sr, and Zn. At the highest Fe oxide to lime ratios, Mn toxicity caused severe yield loss.

Field trials to assess the uptake of arsenic by vegetables from contaminated soils and soil remediation with iron oxides

The uptake of arsenic (As) by plants from contaminated soils presents a health hazard that may affect the use of agricultural and former industrial land. Methods for limiting the hazard are desirable. A proposed remediation treatment comprises the precipitation of iron (Fe) oxides in the contaminated soil by adding ferrous sulfate and lime. The effects on As bioavailability were assessed using a range of vegetable crops grown in the field. Four UK locations were used, where soil was contaminated by As from different sources. At the most contaminated site, a clay loam containing a mean of 748 mg As kg(-1) soil, beetroot, calabrese, cauliflower, lettuce, potato, radish and spinach were grown. For all crops except spinach, ferrous sulfate treatment caused a significant reduction in the bioavailability of As in some part of the crop. Application of ferrous sulfate in solution, providing 0.2% Fe oxides in the soil (0-10 cm), reduced As uptake by a mean of 22%. Solid ferrous sulfate was applied to give concentrations of 0.5% and 1% Fe oxides: the 0.5% concentration reduced As uptake by a mean of 32% and the 1% concentration gave no significant additional benefit. On a sandy loam containing 65 mg As kg(-1) soil, there was tentative evidence that ferrous sulfate treatment up to 2% Fe oxides caused a significant reduction in lettuce As, but calabrese did not respond. At the other two sites, the effects of ferrous sulfate treatment were not significant, but the uptake of soil As was low in treated and untreated soils. Differences between sites in the bioavailable fraction of soil As may be related to the soil texture or the source of As. The highest bioavailability was found on the soil which had been contaminated by aerial deposition and had a high sand content. (C) 2003 Elsevier Science B.V. All rights reserved.

Does speciation impact on Cu uptake by, and toxicity to, the earthworm Eisenia fetida?

Eisenia fetida were exposed to different concentrations (0.009, 0.049 and 0. 125 mg L-1) of Cu in an aqueous medium. Cu speciation was manipulated through the addition of different concentrations (0. 15, 0.35 and 50 mg L-1) of EDTA. Cu speciation (as labile and non-labile pools) was determined using Differential Pulse Anodic Stripping Voltammetry. Labile Cu includes free Cu ions together with weak inorganic Cu complexes and a small fraction of easily dissociable organic complexes. Metal uptake and earthworm mortality increased with total Cu concentration in the EDTA free solutions. In the presence of EDTA both metal uptake and mortality decreased. These experiments demonstrate that Cu speciation governs uptake and consequent toxicity of Cu to E. fetida. (c) 2007 Elsevier Masson SAS. All rights reserved.

Complexation of copper by sewage sludge-derived dissolved organic matter: Effects on soil sorption behaviour and plant uptake

The complexation of Cu by sewage sludge-derived dissolved organic matter (SSDOM) is a process by which the environmental significance of the element may become enhanced due to reduced soil sorption and, hence, increased mobility. The work described in this paper used an ion selective electrode procedure to show that SSDOM complexation of Cu was greatest at intermediate pH values because competition between hydrogen ions and Cu for SSDOM binding sites, and between hydroxyl ions and SSDOM as Cu ligands, was lowest at such values. Batch sorption experiments further showed that the process of Cu complexation by SSDOM provided an explanation for enhanced desorption of Cu from the solid phase of a contaminated, organic matter-rich, clay loam soil, and reduced adsorption of Cu onto the solid phase of a sandy loam soil. Complexation of Cu by SSDOM did not affect uptake of Cu by spring barley plants, when compared to free ionic Cu, in a sand-culture pot experiment. However, it did appear to lead to greater biomass yields of the plant; perhaps indicating that the Cu-SSDOM complex had a lower toxicity towards the plant than the free Cu ion.

Industrial radioactive barite scale: suppression of radium uptake by introduction of competing ions

Incorporation of radioactive isotopes during the formation of barite mineral scale is a widespread phenomenon occurring within the oil, mining and process industries. In a series of experiments radioactive barite/celestite solid solutions (SSBarite-Celcstite) have been synthesized under controlled conditions by the counter diffusion of Ra-226, Ba2+, Sr24+ and SO42- ions through a porous medium (silica gel), to investigate inhibiting effects in Ra uptake associated with the introduction of a competing ion (Sr2+). From characterization studies, the particle size and the morphology of the crystals appear to be related to the initial [Sr]/[Ba] molar ratio of the starting solution. Typically, systems richer in Sr produce smaller sized crystals and clusters characterized by a lower degree of order. The activity introduced to the system is mainly incorporated in the crystals generated from the barite/celestite solid solution as suggested by the activity profiles of the hydrogel columns analysed by gamma-spectrometry. There is a relationship between the initial [Sr]/[Ba] molar ratio of the starting solution and the activity exhibited by the synthesized crystals. An effective inhibition of the Ra-226 uptake during formation of the crystals (SSBarite-Celestite) was obtained through the introduction of a competing ion (Sr2+): the higher the initial [Sr]/[Ba] molar ratio of the starting solution, the lower the intensity of the activity peak in the crystals. (C) 2003 Published by Elsevier Ltd.

A semi-quantitative approach to deriving a model structure for the uptake of organic chemicals by vegetation

An expert elicitation exercise was undertaken to determine those components and processes that are most important for modeling plant uptake of organic chemicals. The state of our knowledge of these processes was also assessed. This semi-quantitative analysis allowed the construction of an idealized model with seven compartments; soil bulk, soil water, roots, stem, leaves, fruit, and air. Three main areas were identified further research: 1) the uptake of organic chemicals by fruit; 2) the internal transfer of organic chemicals between plant structures (e.g., stem and leaves); and 3) the transfer via the soil-air-plant pathway. Until new data becomes available to quantify these processes, it is proposed that an equilibrium partitioning approach is used between plant components other than fruit or that models consist of both an edible and inedible compartment.

Plant uptake of non-ionic organic chemicals

Plant uptake of organic chemicals is an important process when considering the risks associated with land contamination, the role of vegetation in the global cycling of persistent organic pollutants, and the potential for industrial discharges to contaminate the food chain. There have been some significant advances in our understanding of the processes of plant uptake of organic chemicals in recent years; most notably there is now a better understanding of the air to plant transfer pathway, which may be significant for a number of industrial chemicals. This review identifies the key processes involved in the plant uptake of organic chemicals including those for which there is currently little information, e.g., plant lipid content and plant metabolism. One of the principal findings is that although a number of predictive models exist using established relationships, these require further validation if they are to be considered sufficiently robust for the purposes of contaminated land risk assessment or for prediction of the global cycling of persistent organic pollutants. Finally, a number of processes are identified which should be the focus of future research