Nutrient Depletion

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Extracting regulator activity profiles by integration of de novo motifs and expression data : characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor

Extracting regulator activity profiles by integration of de novo motifs and expression data : characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor

Our analysis identified key regulatory profiles and po- tential regulators in each of the experimental time-series. The wt response to phosphate depletion (TS1) is dominated by the exceptional strong activity cluster 7 pattern, the associated regulators being specific to this TS. This cluster includes the PhoP directed repeat PHO box binding site (motif 22), although this motif was present in only 1/2 the targets of this cluster. Our analysis therefore suggests that there are multiple regula- tors besides PhoP with similar profiles, which may be either downstream of the signalling cascade initiated by PhoP, or in parallel. Under glutamate depletion in the wt (TS5) we found a number of motifs with activity localized to nutrient depletion, and weak, or unresponsive to phosphate depletion in TS1/3. This suggests that motifs 6 (homologous to the CRP motif), 12, 13, 15, 25, 38, 54 correspond to specific cascades for carbon or nitrogen limitation, while a number of motifs have an inferred localized activity at/around both phosphate and glutamate depletion in wt suggesting a common stress response: this includes motifs 26, 27 and 35 (homology to E. coli LexA motif). Finally, we found a couple of activity profiles localized at phosphate depletion in the phoP KO: including motifs 11, 29, 33, motif 36 showing a phosphate response in TS1 & 3, while motifs 1, 14, 53 show activity in all time-series at depletion. This analysis indicates that the wt response to phosphate depletion is highly coordinated, primarily through PhoP, while response to glutamate depletion has considerable diversity with a rich range of activity profiles. The weakest signals were found in the phoP KO under phosphate depletion; a small number specific to this case were found, and a couple in common with glutamate depletion. This indicates that in absence of a PhoP response to deal with low phosphate, both a new specific response and a common response to glutamate depletion are triggered.

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Viral infection of marine picoplankton under nutrient depletion conditions : pseudolysogeny and magic spot nucleotides

Viral infection of marine picoplankton under nutrient depletion conditions : pseudolysogeny and magic spot nucleotides

overcome P-stress imposed limitations on the success of infection. In order to examine the possible presence of P-stress related genes in cyanophage, this study examined the infective success of cyanophages isolated from the Gulf of Aqaba, Red Sea under P-deplete conditions. The Gulf of Aqaba represents a marine environment which, due to its geological structure, climate, and its proximity to desert, undergoes interchanging cycles of deep water column mixing during the winter and strong stratification during the summer (Wolf-Vecht, et al., 1992). Winter deep mixing brings nutrients to the photic layer of the water column, enabling primary production. Primary producers, in turn, deplete the photic layer of nutrients during the stratification period, creating oligotrophic conditions in the upper layer of the water column. These interchangeable nutrient levels in the Gulf of Aqaba, make it an interesting study site, since the nutritional status of phytoplankton also changes with changing nutrient conditions, cycling between summer oligotrophs, adapted to low nutrient conditions and winter dominated mesotrophs (Lindell and Post, 1995). Resident bacterial populations respond to stratification and subsequent nutrient depletion, by overexpressing genes that will enable them to either optimize and increase acquisition of the depleted nutrient or by reducing their cellular requirements for this specific nutrient. Previous studies in the Gulf of Aqaba have shown that there is a high correlation between the P-status of the water column and expression of the cyanobacterial phosphate stress-related gene pstS (Fuller, et al., 2005) (Figure 3.1).

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Roots eye view: using microdialysis and microCT to non destructively map root nutrient depletion and accumulation zones

Roots eye view: using microdialysis and microCT to non destructively map root nutrient depletion and accumulation zones

Traditional methods for handling soil microheterogeneity (e.g., lysimeters or potassium chloride extractions) are notably limited (Table 1). In particular, it is unknown how well the measured nutrient levels match root ‐ available nutrients. For example, suction cups (some- times called lysimeters) are biased towards the largest water ‐ filled pores, and salt extraction results vary depending on adsorption to soil particles. Avoiding these limitations, microdialysis samples freely avail- able nutrients and ions in the soil at the root scale giving a more real- istic roots ‐ eye view of the soil environment. Microdialysis can be used repeatedly over time, preserves nutrients in their “ native ” form, and can be used to measure differences in organic or inorganic nutrient forms because microbial activity is blocked at the membrane (Inselsbacher et al., 2011; Miro & Frenzel, 2005).

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BUDGETING PLANT NUTRIENTS FOR OPTIMUM CROP YIELDS AND SOIL FERTILITY MANAGEMENT

BUDGETING PLANT NUTRIENTS FOR OPTIMUM CROP YIELDS AND SOIL FERTILITY MANAGEMENT

Agricultural intensification without adequate restoration of soil fertility may threaten the sustainability of agriculture. Quantitative estimation of plant nutrient depletion from soils is useful for comprehending the state of soil degradation and for devising corrective measures (Harris, 1995). Nutrient-balance exercises serve as instruments to provide indicators of the sustainability of agricultural systems. Nutrient-balance studies have used a variety of approaches and methods for different situations. However, the information has remained scattered in several publications. A recently concluded FAO-commissioned project, „Scaling soil nutrient balances‟, and scientific interactions (FAO, 2003) have thrown further light on the critical issues concerning nutrient-balance assessment approaches. They may also help bridge methodological gaps. Further methodological refinements are feasible through making them more spatially explicit (accounting for spatial variation of soils and climate) and through improving the procedures for calculating nutrient flow and quantifying soil nutrient stocks (David and Ruthven, 1993; Brown and Kane, 1995).

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Spectrochemical determination of unique bacterial responses following long term low level exposure to antimicrobials

Spectrochemical determination of unique bacterial responses following long term low level exposure to antimicrobials

The majority of laboratory studies examining bacterial responses to antimicrobial agents have been in typical laboratory nutrient-rich and short-exposure culture scenarios. How this translates to real-world environmental conditions where bacteria inhabit a nutrient-depleted environment and exposures tend to be long-term remains to be examined. This study applied a non-destructive spectrochemical analysis to examine this question. We demonstrate that exposure time is a major confounding factor in bacterial responses to antimicrobials, as has nutrient depletion. This study has major impact in understanding different bacterial responses to real-world

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Rethink the interlink between land degradation and livelihood of rural communities in Chilga district, Northwest Ethiopia

Rethink the interlink between land degradation and livelihood of rural communities in Chilga district, Northwest Ethiopia

According to Tilahun (2002), a direct link between land degradation and rural livelihood was drawn mainly through three pathways. The first pathway is that the decline in soil fertility as a result of land degradation de- creases farm productivity and income. As crop or livestock production is the major source of household income for rural areas, the decline in soil fertility, through nutrient depletion and poor soil- and water- holding capacity, affects the on-farm income signifi- cantly. The second path is the decline in soil fertility af- fecting the productivity of labor. This is because a degraded land requires much more labor that competes with off-farm income of the households. The last path- way is that land degradation reduces the underground and aboveground biodiversity of the system, which, in turn, affects the biochemical process of the land and the vegetation cover of the land.

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Immunometabolism of pro repair cells

Immunometabolism of pro repair cells

to a tissue-damaged environment have significant bioenergetic and biosynthetic needs. In addition to supporting these needs, metabolic pathways govern the function of pro-repair immune cells, including regulatory T cells and tissue macrophages. In this Review, we explore how specific features of the tissue-damaged environment such as hypoxia, oxidative stress, and nutrient depletion serve as metabolic cues to promote or impair the reparative functions of immune cell populations. Hypoxia, mitochondrial DNA stress, and altered redox balance each contribute to mechanisms regulating the response to tissue damage. For example, hypoxia induces changes in regulatory T cell and macrophage metabolic profiles, including generation of 2-hydroxyglutarate, which inhibits demethylase reactions to modulate cell fate and function. Reactive oxygen species abundant in oxidative environments cause damage to mitochondrial DNA, initiating signaling pathways that likewise control pro-repair cell function. Nutrient depletion following tissue damage also affects pro-repair cell function through metabolic signaling pathways, specifically those sensitive to the redox state of the cell. The study of immunometabolism as an immediate sensor and regulator of the tissue-damaged environment provides opportunities to consider mechanisms that facilitate healthy repair of tissue injury.

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Nutrient and Anti Nutrient Content of Soy Enriched Tapioca

Nutrient and Anti Nutrient Content of Soy Enriched Tapioca

Incorporation of full-fat soy flour into tapioca had vary- ing effects on the nutritional and sensory properties of the product. Soy fortification resulted in improvement of the nutrient composition in terms of protein, fat, energy and mineral contents. Soy enhanced tapioca samples had a low level of anti-nutritional components, making them safe for consumption. However there is need for further toxicological studies on this product. Sample B (85:15) is high in crude protein, crude fiber and has low crude fat which can make it suitable for longer storage periods as the onset of rancidity might take longer periods. It was also found to be the most acceptable sample in terms of its general acceptability. Further studies are also neces- sary to determine protein digestibility; microbial exami- nation and stability studies can be carried out on soy en- hanced tapioca products to determine their safety and their shelf-life. Fortification of tapioca can also be car- ried out by the use soybean meal, soy protein isolate or concentrates in varying substitution levels.

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On the mechanism of rhabdomyolysis in potassium depletion

On the mechanism of rhabdomyolysis in potassium depletion

Rhabdomyolysis and myoglobinuria occur commonly in men who sustain environmental heat injury during intensive physical training in hot climates. These also occur in patients with potassium depletion. Since physical training in hot climates may be accompanied by serious losses of body potassium, the possibility was considered that performance of strenuous exercise when potassium deficient might enhance susceptibility to

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Monoamine depletion by reuptake inhibitors

Monoamine depletion by reuptake inhibitors

While the focus of monoamine reuptake inhibitor depletion is on synaptic monoamine levels, there are other causes of electri- cal dysfunction, such as receptor desensitization and receptor down regulation. While these may be valid topics, they do not apply here. The phenomenon observed here is clearly electrical dysfunction of synaptic origin, whereas receptor desensitiza- tion, receptor down regulation, bundle damage, and so forth, are all postsynaptic processes linked to the postsynaptic neurons. As discussed in the authors’ previous work, there are unique observations that define synaptic electrical dysfunction versus postsynaptic-driven electrical dysfunction. Considerations are as follows. Correcting monoamine depletion-associated syn- aptic electrical dysfunction in the endogenous state involves addressing the problem nutritionally to increase monoamine concentrations from low to normal. 7,8,11–16,20–22 Correcting

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Effect of Sodium Chloride on Subsequent Survival of Staphylococcus aureus in Various Preservatives

Effect of Sodium Chloride on Subsequent Survival of Staphylococcus aureus in Various Preservatives

For control experiments, 0.5 ml of the overnight grown bacterial culture was directly added to flasks containing 30 ml nutrient broth plus 20% NaCl, nutrient broth plus 0.3% Thymus vulgaris extract, or nutrient broth plus 0.1% ascorbic acid; and flasks were incubated static at 37˚C for 4 days. For growth at low temperature (control expe- riment), 0.5 ml of the overnight grown bacterial culture was directly added to flask containing 30 ml nutrient broth alone and incubated at 5˚C for 12 days. Number of vi- able cells was enumerated as mentioned above.

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Potential structural role of non coding and coding RNAs in the
organization of the cytoskeleton at the vegetal cortex of Xenopus
oocytes

Potential structural role of non coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes

Fig. 12. Models of the effect of depletion of Xlsirts and VegT RNAs on the cytokeratin network and germinal granules. (A) The effect of Xlsirts RNA and VegT mRNA depletion, and of anti-cytokeratin antibody on the cytokeratin network and the germinal granules. In the cortex of stage VI oocytes, the cytokeratin (green) forms a complex, multi-layer network. The particles of VegT mRNA (red) and Xlsirts RNA (blue) are integrated into the network in RNA- specific pattern (1). The ablation of VegT mRNA or injection of anti- pancytokeratin antibody causes a severance of the network (2), which in turn, results in a premature aggregation of the germinal granules (3). The ablation of Xlsirts RNA results in the collapse of the network into a flattened, less complex sheet (2). The means of association of cytokeratin with germinal granules are unknown, but one possibility is that cytokeratin anchors germinal granules (pink spheres) indirectly, via an unknown binding protein(s) (yellow, 3). (B) The effect of VegT mRNA depletion and anti-cytokeratin antibody on the cytokeratin network and the germinal granule aggregation in oocytes and embryos. Control (left panel), and antisense VegT ODN or anti-cytokeratin C11 antibody injected (right panel) oocytes and embryos. Part of the vegetal cortex is shown. For simplicity, the cytokeratin is shown only in part of the cortex. In stage VI control oocytes, the germinal granules (pink spheres) are located in germ plasm islands (yellow) within the cortical network of cytokeratin filaments (green). In antisense VegT and anti-

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AN EOQ INVENTORY MODEL USING RAMP TYPE DEMAND WITH DETERIORATION AND SHORTAGES

AN EOQ INVENTORY MODEL USING RAMP TYPE DEMAND WITH DETERIORATION AND SHORTAGES

In earlier days classical inventory model like Harris [1] assumes that the depletion of inventory is due to a constant demand rate. But subsequently, it was noticed that depletion of inventory may take place due to deterioration also, and then the problem of decision makers is how to control and maintain inventories of deteriorating items. Many researchers like Ghare and Schrader [2], Goyal et al. [3], Covert and Philip [4], Aggrawal and Jaggi [5], Cohen [6], Mishra [7] are very important in this connection. As the time progressed, several other researchers developed inventory models with deteriorating items with time dependent demand rates. In this connection, related works may refer to Ritchie [8], Hariga [9], S.P.Singh and V.K.Sehgal [10] Ghose and Chaudhari [11], Donaldson [12], Silver [13], Datta and pal [14], Deb and Chaudhari [15], Pal and mandal [16], Goel and Aggrawal [17]. Mishra [7] developed a two parameter Weibull distribution deterioration for an inventory model. This was followed by many researchers like S.P.Singh and G.C.Panda [18] Dev and Patel [19], Shah and Jaiswal [20], Giri et al. [21] etc. In the present paper, we drive the three EOQ inventory models for items that deteriorate at a Weibull rate, assuming the demand rate with a ramp type function of time. Shortages are allowed. The demand rate for such items increases with time up to certain time and then ultimately stabilizes and becomes constant. Finally numerical examples are proposed to demonstrate our developed model and the solution procedure.

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Depletion of nonlinearity in the pressure force driving Navier Stokes flows : nonlinear depletion in NS flows

Depletion of nonlinearity in the pressure force driving Navier Stokes flows : nonlinear depletion in NS flows

Given the apparent inadequacy of viscous effects in regularising Navier–Stokes flows [38], re- searchers have looked for the possibility of nonlinear depletion in the vortex dynamics. Such de- pletion is a well-documented phenomenon for both Euler and Navier–Stokes cases [1, 6, 17, 21, 24, 30, 31, 34]. The question is how to capture and exploit this favourable phenomenon in a rigorous manner. A recent investigation by Donzis et al. [17] has addressed this question in some detail.

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Optimization of Water and Nutrient Supply during Stock Plant Production and Propagation of Vegetative Cuttings.

Optimization of Water and Nutrient Supply during Stock Plant Production and Propagation of Vegetative Cuttings.

Neither zonal geranium nor petunia cuttings soluble sugar concentrations were affected by nutrient treatment. These results are contradictory to the 2009 study by Zerche and Druege reporting N supply (low, adequate, and high N rates based on biweekly soil sample analysis results) affected carbohydrate levels in poinsettia cuttings. The observation that soluble carbohydrate levels in the leaf lamina accumulated during rooting is likely related to depletion during shipping. Depletion is thought to up-regulate genes involved in photosynthesis, remobilization, and carbohydrate export (Koch, 1996). Our results in petunia, with the exception of sucrose, support research by Ahkami et al (2008). Glucose and fructose levels reached their highest before the emergence of roots. Petunia cutting sucrose levels in this study do not appear to have been depleted during shipping and did not have the same response as the other soluble carbohydrates.

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Roles of Capsid-Interacting Host Factors in Multimodal Inhibition of HIV-1 by PF74

Roles of Capsid-Interacting Host Factors in Multimodal Inhibition of HIV-1 by PF74

were significantly changed in all of the ranges we tested (Fig. 8C to E) except for the highest range of PF74 concentrations (Fig. 8F). Importantly, CypA differed from CPSF6 in the midrange of drug concentrations, where CypA depletion significantly increased the magnitude of inhibition by PF74 (Fig. 8D). This was also observed when slope values for the same drug range were examined: CypA- depleted cells displayed an m value of 3.83 ⫾ 1.38, which was higher than the m value (1.3 ⫾ 0.95) derived on control cells. Thus, it appeared that CypA depletion shifted the steep slope to- ward lower drug concentrations. Substantially similar observa- tions were made when CypA-CA interactions were blocked with cyclosporine (CsA) and by G89V and P90A mutations within CA (Fig. 9A and B). Namely, both CsA treatment (Fig. 9A) and the G89V and P90A mutations (Fig. 9B) removed the triphasic dose- response curve and increased the magnitude of inhibition at me- dium concentrations. These changes in the curves were also ob- served when inocula of CA mutants were normalized by infectivity to that of the WT virus. Importantly, this finding was observed using cell clones in which the PPIA gene was knocked out by using CRISPR-Cas9 technology (Fig. 9C to E). CypA knockout eliminated the unique triphasic dose-response curve (Fig. 9D) and increased the potency of high PF74 concentrations, which was observed in an experimental setting using higher virus input (Fig. 9E). Importantly, reverse complementation of CypA expression restored the antiviral activity at lower concentrations FIG 8 CypA depletion alters the dose-response curve of PF74 in a unique manner. Control (nontargeting-siRNA-treated [Ctrl]) or CypA-depleted cells (CypA k/d) were used for a single-cycle infection assay using luciferase-encoding reporter virus. (A) Western blot detection of HeLa cells transfected with nontargeting siRNA or siRNA targeting CypA. (B) Infectivity values relative to the result with no drug are plotted to display PF74’s antiviral activity. Mean values from four independent experiments are shown, with error bars denoting the standard errors of the means. (C to F) The magnitudes of PF74-mediated inhibition of HIV-1 in control cells were compared to the levels of inhibition in CypA- or CPSF6-depleted cells by plotting the decreases in viral infectivity between various ranges of drug concentrations. Each dot represents the value for one experiment, and the bars denote the means of the groups. **, P ⬍ 0.01; *, P ⬍ 0.05.

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Ozone Layer Depletion

Ozone Layer Depletion

Chlorofluorocarbons Ozone depletion occurs when the natural balance between the production and destruction of stratospheric ozone is disturbed. Although natural phenomenon can cause ozone depletion but human activities such as CFCs are now accepted as major cause of depletion. All ozone depleting chemicals contain chlorine and bromine. CFCs are highly volatile and non combustible so they are very quickly evaporated and can easily reach in stratosphere where ozone is present here they start depleting ozone molecules. These CFCs have also adverse affects on human health . According to the chemical model for ozone destruction proposed about 20 years ago, the photolysis of Cl2O2 is key to ozone depletion reaction. But now atmospheric researchers studied that the rate of this reaction is not extremely high as it was thought previously so we can no longer say that CFCs are the main cause of ozone depletion .

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Depletion and social reproduction

Depletion and social reproduction

The depletion here is societal as well as individual and for households. It is noticeable that the old community bonds and inputs, and reciprocal care, are breaking down in the face of the new circumstances, though women still bear the brunt of ‘managing crisis’. According to Waring, detailed time use surveys on a regular basis, contextualised with other similar data, are the only way of encapsulating this situation. Interestingly, she is not in favour of a monetary valuation of the unpaid work, seeing this as an abstraction from the real situation. Following from the distinction made above, the monetary valuation of unpaid work would mitigate depletion but is in itself some way off in either replenishing depleting bodies and social networks or transforming the structural conditions in which the subjects of this study are deemed invisible as producers. This is a point we may wish to consider.

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A. Data Characteristics

A. Data Characteristics

In this paper, we present the analysis results of survival rate estimation of population in Thailand, comparing to the survival rate to age 65 of people in China. The predictive attributes used in our study are environment factors, health expenditure, natural resource depletion, energy and mineral depletion, carbon dioxide (CO 2 ) emissions from gas, liquid,

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Algal motility in variable turbulence

Algal motility in variable turbulence

Strong vertical mixing could overcome the swimming efforts of dinoflagellates and move them out of the euphotic zone as well as produce other detrimental effects (see Section 1.6). This might explain why diatoms and dinoflagellates are often found to be mutually exclusive in the environment. Diatoms, in general, are more ‘robust’ than dinoflagellates, they can grow faster (Smayda, 1997), they have lower respiration rates than dinoflagellates and therefore survive longer in the dark (approx. 8 days for dinoflagellates compared to approx. 40 days for diatoms) (Broekhuizen, 1999). What is thus the reason for their success considering that they have apparently been endowed with less favourable qualities? Many dinoflagellate species are capable of mixotrophy or are outright heterotrophs. The autotrophic species have generally lower light requirements than diatoms to achieve their maximum photosynthetic rate. Their slow growth rate enables them to adapt better to low light conditions and they are able to utilise low ambient nutrient concentrations, outcompeting diatoms in the oligotrophic waters of the tropics and many other nutrient limited regions of the world oceans. Some species produce allelochemicals to repel predators and competitors (‘harmful algal blooms’), and last but maybe not least, they are much more motile than other algal taxa. This might help them realise population growth rates which are similar to those of diatoms (Broekhuizen, 1999).

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