672 research outputs found
Dynamic Image-Based Modelling of Kidney Branching Morphogenesis
Kidney branching morphogenesis has been studied extensively, but the
mechanism that defines the branch points is still elusive. Here we obtained a
2D movie of kidney branching morphogenesis in culture to test different models
of branching morphogenesis with physiological growth dynamics. We carried out
image segmentation and calculated the displacement fields between the frames.
The models were subsequently solved on the 2D domain, that was extracted from
the movie. We find that Turing patterns are sensitive to the initial conditions
when solved on the epithelial shapes. A previously proposed diffusion-dependent
geometry effect allowed us to reproduce the growth fields reasonably well, both
for an inhibitor of branching that was produced in the epithelium, and for an
inducer of branching that was produced in the mesenchyme. The latter could be
represented by Glial-derived neurotrophic factor (GDNF), which is expressed in
the mesenchyme and induces outgrowth of ureteric branches. Considering that the
Turing model represents the interaction between the GDNF and its receptor RET
very well and that the model reproduces the relevant expression patterns in
developing wildtype and mutant kidneys, it is well possible that a combination
of the Turing mechanism and the geometry effect control branching
morphogenesis
The enzymatic activity of the VEGFR2-receptor for the biosynthesis of dinucleoside polyphosphates
The group of dinucleoside polyphosphates encompasses a large number of molecules consisting of two nucleosides which are connected by a phosphate chain of variable length. While the receptors activated by dinucleoside polyphosphates as well as their degradation have been studied in detail, its biosynthesis has not been elucidated so far. Since endothelial cells released the dinucleoside polyphosphate uridine adenosine tetraphosphate (Up4A), we tested cytosolic proteins of human endothelial cells obtained from dermal vessels elicited for enzymatic activity. When incubated with ADP and UDP, these cells showed increasing concentrations of Up4A. The underlying enzyme was isolated by chromatography and the mass spectrometric analysis revealed that the enzymatic activity was caused by the vascular endothelial growth factor receptor 2 (VEGFR2). Since VEGFR2 but neither VEGFR1 nor VEGFR3 were capable to synthesise dinucleoside polyphosphates, Tyr-1175 of VEGFR2 is most likely essential for the enzymatic activity of interest. Further, VEGFR2-containing cells like HepG2, THP-1 and RAW264.7 were capable of synthesising dinucleoside polyphosphates. VEGFR2-transfected HEK 293T/17 but not native HEK 293T/17 cells synthesised dinucleoside polyphosphates in vivo too. The simultaneous biosynthesis of dinucleoside polyphosphates could amplify the response to VEGF, since dinucleoside polyphosphates induce cellular growth via P2Y purinergic receptors. Thus the biosynthesis of dinucleoside polyphosphates by VEGFR2 may enhance the proliferative response to VEGF. Given that VEGFR2 is primarily expressed in endothelial cells, the biosynthesis of dinucleoside polyphosphates is mainly located in the vascular system. Since the vasculature is also the main site of action of dinucleoside polyphosphates, activating vascular purinoceptors, blood vessels appear as an autocrine system with respect to dinucleoside polyphosphates. We conclude that VEGFR2 receptor is capable of synthesising dinucleoside polyphosphates. These mediators may modulate the effects of VEGFR2 due to their proliferative effects
Perspectives for sustainable aviation biofuels in Brazil
The aviation industry has set ambitious goals to reduce carbon emissions in coming decades. The strategy involves the use of sustainable biofuels, aiming to achieve benefits from environmental, social, and economic perspectives. In this context, Brazilian conditions are favorable, with a mature agroindustry that regularly produces automotive biofuel largely adopted by Brazilian road vehicles, while air transportation has been growing at an accelerating pace and a modern aircraft industry is in place. This paper presents the main conclusions and recommendations from a broad assessment of the technological, economic, and sustainability challenges and opportunities associated with the development of drop-in aviation biofuels in Brazil. It was written by a research team that prepared the initial reports and conducted eight workshops with the active participation of more than 30 stakeholders encompassing the private sector, government institutions, NGOs, and academia. The main outcome was a set of guidelines for establishing a new biofuels industry, including recommendations for (a) filling the identified research and development knowledge gaps in the production of sustainable feedstock; (b) overcoming the barriers in conversion technology, including scaling-up issues; (c) promoting greater involvement and interaction between private and government stakeholders; and (d) creating a national strategy to promote the development of aviation biofuels2015FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP2012/50009-
Congenital deficiency reveals critical role of ISG15 in skin homeostasis
Ulcerating skin lesions are manifestations of human ISG15 deficiency, a type I interferonopathy. However, chronic inflammation may not be their exclusive cause. We describe two siblings with recurrent skin ulcers that healed with scar formation upon corticosteroid treatment. Both had a homozygous nonsense mutation in the ISG15 gene, leading to unstable ISG15 protein lacking the functional domain. We characterized ISG15(-/-) dermal fibroblasts, HaCaT keratinocytes, and human induced pluripotent stem cell-derived vascular endothelial cells. ISG15-deficient cells exhibited the expected hyperinflammatory phenotype, but also dysregulated expression of molecules critical for connective tissue and epidermis integrity, including reduced collagens and adhesion molecules, but increased matrix metalloproteinases. ISG15(-/-) fibroblasts exhibited elevated ROS levels and reduced ROS scavenger expression. As opposed to hyperinflammation, defective collagen and integrin synthesis was not rescued by conjugation-deficient ISG15. Cell migration was retarded in ISG15(-/-) fibroblasts and HaCaT keratinocytes, but normalized under ruxolitinib treatment. Desmosome density was reduced in an ISG15(-/-) 3D epidermis model. Additionally, there were loose architecture and reduced collagen and desmoglein expression, which could be reversed by treatment with ruxolitinib/doxycycline/TGF-beta 1. These results reveal critical roles of ISG15 in maintaining cell migration and epidermis and connective tissue homeostasis, whereby the latter likely requires its conjugation to yet unidentified targets
Citraconate inhibits ACOD1 (IRG1) catalysis, reduces interferon responses and oxidative stress, and modulates inflammation and cell metabolism
Although the immunomodulatory and cytoprotective properties of itaconate have been studied extensively, it is not known
whether its naturally occurring isomers mesaconate and citraconate have similar properties. Here, we show that itaconate
is partially converted to mesaconate intracellularly and that
mesaconate accumulation in macrophage activation depends
on prior itaconate synthesis. When added to human cells in
supraphysiological concentrations, all three isomers reduce
lactate levels, whereas itaconate is the strongest succinate
dehydrogenase (SDH) inhibitor. In cells infected with influenza A virus (IAV), all three isomers profoundly alter amino
acid metabolism, modulate cytokine/chemokine release and
reduce interferon signalling, oxidative stress and the release
of viral particles. Of the three isomers, citraconate is the
strongest electrophile and nuclear factor-erythroid 2-related
factor 2 (NRF2) agonist. Only citraconate inhibits catalysis of
itaconate by cis-aconitate decarboxylase (ACOD1), probably
by competitive binding to the substrate-binding site. These
results reveal mesaconate and citraconate as immunomodulatory, anti-oxidative and antiviral compounds, and citraconate
as the first naturally occurring ACOD1 inhibitor
Citraconate inhibits ACOD1 (IRG1) catalysis, reduces interferon responses and oxidative stress, and modulates inflammation and cell metabolism
Although the immunomodulatory and cytoprotective properties of itaconate have been studied extensively, it is not known whether its naturally occurring isomers mesaconate and citraconate have similar properties. Here, we show that itaconate is partially converted to mesaconate intracellularly and that mesaconate accumulation in macrophage activation depends on prior itaconate synthesis. When added to human cells in supraphysiological concentrations, all three isomers reduce lactate levels, whereas itaconate is the strongest succinate dehydrogenase (SDH) inhibitor. In cells infected with influenza A virus (IAV), all three isomers profoundly alter amino acid metabolism, modulate cytokine/chemokine release and reduce interferon signalling, oxidative stress and the release of viral particles. Of the three isomers, citraconate is the strongest electrophile and nuclear factor-erythroid 2-related factor 2 (NRF2) agonist. Only citraconate inhibits catalysis of itaconate by cis-aconitate decarboxylase (ACOD1), probably by competitive binding to the substrate-binding site. These results reveal mesaconate and citraconate as immunomodulatory, anti-oxidative and antiviral compounds, and citraconate as the first naturally occurring ACOD1 inhibitor. [Image: see text
Imbibition in Disordered Media
The physics of liquids in porous media gives rise to many interesting
phenomena, including imbibition where a viscous fluid displaces a less viscous
one. Here we discuss the theoretical and experimental progress made in recent
years in this field. The emphasis is on an interfacial description, akin to the
focus of a statistical physics approach. Coarse-grained equations of motion
have been recently presented in the literature. These contain terms that take
into account the pertinent features of imbibition: non-locality and the
quenched noise that arises from the random environment, fluctuations of the
fluid flow and capillary forces. The theoretical progress has highlighted the
presence of intrinsic length-scales that invalidate scale invariance often
assumed to be present in kinetic roughening processes such as that of a
two-phase boundary in liquid penetration. Another important fact is that the
macroscopic fluid flow, the kinetic roughening properties, and the effective
noise in the problem are all coupled. Many possible deviations from simple
scaling behaviour exist, and we outline the experimental evidence. Finally,
prospects for further work, both theoretical and experimental, are discussed.Comment: Review article, to appear in Advances in Physics, 53 pages LaTe
Quantum mechanical studies of lincosamides
Lincosamides are a class of antibiotics used both in clinical and veterinary practice for a wide range of pathogens. This group of drugs inhibits the activity of the bacterial ribosome by binding to the 23S RNA of the large ribosomal subunit and blocking protein synthesis. Currently, three X-ray structures of the ribosome in complex with clindamycin are available in the Protein Data Bank, which reveal that there are two distinct conformations of the pyrrolidinyl propyl group of the bound clindamycin. In this work, we used quantum mechanical methods to investigate the probable conformations of clindamycin in order to explain the two binding modes in the ribosomal 23S RNA. We studied three lincosamide antibiotics: clindamycin, lincomycin, and pirlimycin at the B3LYP level with the 6-31G** basis set. The focus of our work was to connect the conformational landscape and electron densities of the two clindamycin conformers found experimentally with their physicochemical properties. For both functional conformers, we applied natural bond orbital (NBO) analysis and the atoms in molecules (AIM) theory, and calculated the NMR parameters. Based on the results obtained, we were able to show that the structure with the intramolecular hydrogen bond C=O…H–O is the most stable conformer of clindamycin. The charge transfer between the pyrrolidine-derivative ring and the six-atom sugar (methylthiolincosamide), which are linked via an amide bond, was found to be the dominant factor influencing the high stability of this conformer
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