scholarly journals New Insights on Arabidopsis thaliana Root Adaption to Ammonium Nutrition by the Use of a Quantitative Proteomic Approach

2019 ◽  
Vol 20 (4) ◽  
pp. 814 ◽  
Author(s):  
Inmaculada Coleto ◽  
Izargi Vega-Mas ◽  
Gaetan Glauser ◽  
María González-Moro ◽  
Daniel Marino ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Metabolic Pathways ◽  
Inorganic Nitrogen ◽  
Essential Element ◽  
Nitrous Oxide Emissions ◽  
Stressful Situation ◽  
Ph Homeostasis ◽  
Proteomic Approach ◽  
Wide Range ◽  
Ammonium Nutrition

Nitrogen is an essential element for plant nutrition. Nitrate and ammonium are the two major inorganic nitrogen forms available for plant growth. Plant preference for one or the other form depends on the interplay between plant genetic background and environmental variables. Ammonium-based fertilization has been shown less environmentally harmful compared to nitrate fertilization, because of reducing, among others, nitrate leaching and nitrous oxide emissions. However, ammonium nutrition may become a stressful situation for a wide range of plant species when the ion is present at high concentrations. Although studied for long time, there is still an important lack of knowledge to explain plant tolerance or sensitivity towards ammonium nutrition. In this context, we performed a comparative proteomic study in roots of Arabidopsis thaliana plants grown under exclusive ammonium or nitrate supply. We identified and quantified 68 proteins with differential abundance between both conditions. These proteins revealed new potential important players on root response to ammonium nutrition, such as H+-consuming metabolic pathways to regulate pH homeostasis and specific secondary metabolic pathways like brassinosteroid and glucosinolate biosynthetic pathways.

scholarly journals Soil Nitrogen Dynamics in a Managed Temperate Grassland Under Changed Climatic Conditions

Water ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 931
Author(s):  
Mona Giraud ◽  
Jannis Groh ◽  
Horst H. Gerke ◽  
Nicolas Brüggemann ◽  
Harry Vereecken ◽  
...  
Keyword(s):  
Nitrogen Uptake ◽  
Inorganic Nitrogen ◽  
Nitrogen Concentration ◽  
Nitrogen Dynamics ◽  
Climatic Conditions ◽  
Undisturbed Soil ◽  
Nitrogen Emissions ◽  
Growing Period ◽  
Grassland Type ◽  
Wide Range

Grasslands are one of the most common biomes in the world with a wide range of ecosystem services. Nevertheless, quantitative data on the change in nitrogen dynamics in extensively managed temperate grasslands caused by a shift from energy- to water-limited climatic conditions have not yet been reported. In this study, we experimentally studied this shift by translocating undisturbed soil monoliths from an energy-limited site (Rollesbroich) to a water-limited site (Selhausen). The soil monoliths were contained in weighable lysimeters and monitored for their water and nitrogen balance in the period between 2012 and 2018. At the water-limited site (Selhausen), annual plant nitrogen uptake decreased due to water stress compared to the energy-limited site (Rollesbroich), while nitrogen uptake was higher at the beginning of the growing period. Possibly because of this lower plant uptake, the lysimeters at the water-limited site showed an increased inorganic nitrogen concentration in the soil solution, indicating a higher net mineralization rate. The N2O gas emissions and nitrogen leaching remained low at both sites. Our findings suggest that in the short term, fertilizer should consequently be applied early in the growing period to increase nitrogen uptake and decrease nitrogen losses. Moreover, a shift from energy-limited to water-limited conditions will have a limited effect on gaseous nitrogen emissions and nitrate concentrations in the groundwater in the grassland type of this study because higher nitrogen concentrations are (over-) compensated by lower leaching rates.

P0031AURINE METABOLOMICS: AN EMERGING TOOL FOR DISSECTING BIOLOGICAL ABERRATIONS UNDERLYING RENAL DYSFUNCTION IN BARDET-BIEDL SYNDROME

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Miriam Zacchia ◽  
Emanuela Marchese ◽  
Marianna Caterino ◽  
Margherita Ruoppolo ◽  
Giovambattista Capasso
Keyword(s):  
Lactic Acid ◽  
Kidney Disease ◽  
Renal Disease ◽  
Renal Dysfunction ◽  
Metabolic Pathways ◽  
Healthy Subjects ◽  
Hexadecenoic Acid ◽  
Kidney Dysfunction ◽  
Bardet Biedl Syndrome ◽  
Wide Range

Abstract Background and Aims Bardet Biedl Syndrome (BBS) is a rare genetic disorder characterized by a wide range of organ dysfunction, including kidney disease. The severity of renal dysfunction is highly variable in this setting, ranging from tubular defects to the end stage renal disease, with poor genotype-phenotype correlation. Proteomics and metabolomics are powerful tools able to contribute to the better understanding of molecular basis of disease conditions. Our previous studies demonstrated that the urinary proteomic pattern of BBS patients differed from that of healthy subjects, with a set of deregulated proteins including cell adhesion and extracellular matrix organization proteins (1). The present study aims to characterize urine metabolomic profile of BBS patients, in order to identify both 1) potential disease biomarkers and 2) aberrant metabolic pathways underlying renal disease Method To this end, in the pilot study urine samples have been collected from 14 adult BBS patients and have been compared with healthy volunteers, using an untargeted strategy. In the confirmation study, 24 BBS patients with wide range of kidney dysfunction have been enrolled, and additional control groups, besides healthy subjects, were included: 1) age-gender-matched chronic kidney disease patients by other causes and 2) obese individuals. Results Several metabolites were de-regulated in BBS patients compared with normal subjects (lactic acid, glycolic acid,3-Hydroxypropionic acid, pyruvic acid, 3-hydroxyisobutyric acid, 2-ethyl-3-hydroxy-propionic acid, succinic acid, fumaric acid, erythropentonic acid, 2-hydroxyglutaric acid, 4-hydroxyphenyllactic acid, 3,4-pyridinedicarboxylic acid, retinoic acid, 4-hydroxyphenylacetic acid, palmitic acid, 9-Hexadecenoic acid, oleic acid and 9-Octadecenoic acid). The clusterization performed by MetaboAnalyst tool, revealed a possible deregulation of different metabolic pathways, including glycolysis, TCA cycle, pyruvate metabolism, lipids biosynthesis and glutamate metabolism (p-value <0.01) (figure 1); some of these pathways were described as de-regulated in other ciliopathies (2). In the confirmation study (on-going studies) some metabolites, including lactic acid and intermediates of Krebs cycle, correlated with kidney dysfunction only in the BBS group. Conclusion These findings suggest that urine metabolomic fingerprint of BBS patients is different from that of healthy subjects and indicate a possible deregulation of several metabolic pathways; some urinary molecules correlated with kidney dysfunction only in BBS patients, suggesting the specificity of these results.

scholarly journals Development of cancer metabolism as a therapeutic target: new pathways, patient studies, stratification and combination therapy

2019 ◽  
Vol 122 (1) ◽  
pp. 1-3 ◽  
Author(s):  
Adrian L. Harris
Keyword(s):  
Metabolic Pathways ◽  
Trial Design ◽  
Cancer Metabolism ◽  
Aerobic Glycolysis ◽  
Critical Role ◽  
Therapeutic Approaches ◽  
Preclinical Models ◽  
Wide Range ◽  
Patient Studies

AbstractCancer metabolism has undergone a resurgence in the last decade, 70 years after Warburg described aerobic glycolysis as a feature of cancer cells. A wide range of techniques have elucidated the complexity and heterogeneity in preclinical models and clinical studies. What emerges are the large differences between tissues, tumour types and intratumour heterogeneity. However, synergies with inhibition of metabolic pathways have been found for many drugs and therapeutic approaches, and a critical role of window studies and translational trial design is key to success.

scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

TETRASPORE is required for male meiotic cytokinesis in Arabidopsis thaliana

Development ◽  
1997 ◽  
Vol 124 (13) ◽  
pp. 2645-2657 ◽  
Author(s):  
M. Spielman ◽  
D. Preuss ◽  
F.L. Li ◽  
W.E. Browne ◽  
R.J. Scott ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Pollen Development ◽  
Male Meiosis ◽  
Pollen Grain ◽  
Flowering Plants ◽  
External Wall ◽  
Normal Pollen ◽  
Wide Range ◽  
Asymmetric Divisions ◽  
And Function

In flowering plants, male meiosis occurs in the microsporocyte to produce four microspores, each of which develops into a pollen grain. Here we describe four mutant alleles of TETRASPORE (TES), a gene essential for microsporocyte cytokinesis in Arabidopsis thaliana. Following failure of male meiotic cytokinesis in tes mutants, all four microspore nuclei remain within the same cytoplasm, with some completing their developmental programmes to form functional pollen nuclei. Both of the mitotic divisions seen in normal pollen development take place in tes mutants, including the asymmetric division required for the differentiation of gametes; some tes grains perform multiple asymmetric divisions in the same cytoplasm. tes pollen shows a variety of abnormalities subsequent to the cytokinetic defect, including fusion of nuclei, formation of ectopic internal walls, and disruptions to external wall patterning. In addition, ovules fertilized by tes pollen often abort, possibly because of excess paternal genomes in the endosperm. Thus tes mutants not only reveal a gene specific to male meiosis, but aid investigation of a wide range of processes in pollen development and function.

scholarly journals Interaction among Controlling Factors on Riverine DIN Export in Small Mountainous Rivers of Taiwan: Inseparable Human-Landscape System

Water ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2981
Author(s):  
Wen-Shiuan Lee ◽  
Jr-Chuan Huang ◽  
Chung-Te Chang ◽  
Shih-Chien Chan ◽  
Ying-San Liou ◽  
...  
Keyword(s):  
Inorganic Nitrogen ◽  
Seasonal Pattern ◽  
Water Quality Management ◽  
Negative Relationship ◽  
Dry Season ◽  
Mitigation Strategies ◽  
Minor Effect ◽  
Dominant Form ◽  
Wide Range ◽  
Human Landscape

Increasing anthropogenic nitrogen (N) emission via different pathways has shown prominent impact on aquatic ecosystems for decades, but the effects of interaction among climate-, landscape- and human-associated variables on riverine DIN (dissolved inorganic nitrogen, mainly NO3− and NH4+) export are unclear. In this study, the data of 43 watersheds with a wide range of climate-, landscape- and human-associated gradients across Taiwan were evaluated with partial redundancy analysis (pRDA) to examine their interactive controls on riverine DIN export. Results show that the annual riverine DIN export in Taiwan is approximately 3100 kg-N km−2 yr−1, spanning from 230 kg-N km−2 yr−1 in less disturbed watersheds (eastern and central Taiwan) to 10,000 kg-N km−2 yr−1 in watersheds with intensive human intervention (southwestern and northern Taiwan). NO3− is generally the single dominant form of DIN, while NH4+ renders significance in disturbed watersheds. Nearly all environmental variables display a positive correlation with DIN export, except for landscape setting variables (e.g., slope, area, channel length), which show a negative relationship. In terms of seasonal pattern, climate and human-landscape variables are related to NO3− export independently in the wet season, yet in the dry season climate-human variables jointly dominate NO3− export. Meanwhile, human-landscape (LH) variables (λ1 of LH > 0.60) control NH4+ exports in both seasons, and human-associated (H) variables (λ1 of H = 0.13) have a minor effect on NH4+ exports in dry season. Precisely, the contribution of controlling variables on DIN export vary with species and seasons, indicating water quality management could be time-dependent, which should be taken into consideration for designing mitigation strategies.

scholarly journals Limits to the European Commission – Managing Services of General Interests

2013 ◽  
Vol 4 (3) ◽  
pp. 23-48 ◽  
Author(s):  
Jerzy Ząbkowicz
Keyword(s):  
European Commission ◽  
Essential Element ◽  
Shared Responsibility ◽  
General Interest ◽  
Regulatory Regime ◽  
The European Union ◽  
Public Authorities ◽  
Wide Range ◽  
Services Of General Interest ◽  
The Eu

Services of general interest form an essential element of the European model of society as a way to increase quality of life and to overcome social exclusion and isolation. They are also at the core of the public debate touching the central question of the role public authorities and the institutions of the European Union play in a market economy. The competencies and responsibilities conferred by the Treaty, the EU regulations and directives lay emphasis on the essential role and the wide discretion of national, regional and local authorities in defining, organizing, financing and monitoring services of general interest. The same time the EU Law provide the European Commission with a wide range of means of action to ensure the compliance of the process of organizing and financing such services according to a comprehensive regulatory regime at Community level to make them compatible with the internal market and to prevent a distortion of the competition rules. The paper indicates divergences of the points of view of public authorities and the Commission on their role, shared responsibility and powers in that process.

scholarly journals Fluorescence lifetime imaging of pH along the secretory pathway

2021 ◽  
Author(s):  
Peter Linders ◽  
Martin ter Beest ◽  
Geert van den Bogaart
Keyword(s):  
Temporal Resolution ◽  
Fluorescence Lifetime ◽  
Secretory Pathway ◽  
Fluorescent Protein ◽  
Excitation Wavelength ◽  
Fluorescence Lifetime Imaging ◽  
Ph Homeostasis ◽  
Ph Changes ◽  
Lifetime Imaging ◽  
Wide Range

Many cellular processes are dependent on correct pH levels, and this is especially important for the secretory pathway. Defects in pH homeostasis in distinct organelles cause a wide range of diseases, including disorders of glycosylation and lysosomal storage diseases. Ratiometric imaging of the pH-sensitive mutant of green fluorescent protein (GFP), pHLuorin, has allowed for targeted pH measurements in various organelles, but the required sequential image acquisition is intrinsically slow and therefore the temporal resolution unsuitable to follow the rapid transit of cargo between organelles. We therefore applied fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar pH with just a single excitation wavelength. We first validated this method by confirming the pH in multiple compartments along the secretory pathway. Then, we analyze the dynamic pH changes within cells treated with Brefeldin A, a COPI coat inhibitor. Finally, we followed the pH changes of newly-synthesized molecules of the inflammatory cytokine tumor necrosis factor (TNF)-α while it was in transit from the endoplasmic reticulum via the Golgi to the plasma membrane. The toolbox we present here can be applied to measure intracellular pH with high spatial and temporal resolution, and can be used to assess organellar pH in disease models.

scholarly journals Computational modeling of anthocyanin pathway evolution

2019 ◽  
Author(s):  
Lucas C. Wheeler ◽  
Stacey D. Smith
Keyword(s):  
Metabolic Pathways ◽  
Flower Color ◽  
Complex Phenotype ◽  
Pathway Evolution ◽  
Anthocyanin Pathway ◽  
Trade Offs ◽  
Wide Range ◽  
Pathway Function ◽  
Simple Kinetic Model ◽  
New Mutations

AbstractAlteration of metabolic pathways is a key component of the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentaion pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a realistic, functional set of parameters. We then stochastically evolved the pathway toward a defined optimum and and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examine whether the observed trajectories and constraints help to explain experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework which can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.

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