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1.
Plant Cell ; 36(3): 642-664, 2024 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-38016103

RESUMO

Many non-graminaceous species release various coumarins in response to iron (Fe) deficiency. However, the physiological relevance of these coumarins remains poorly understood. Here, we show that the three enzymes leading to sideretin biosynthesis co-exist in Arabidopsis (Arabidopsis thaliana) epidermal and cortical cells and that the shift to fraxetin at alkaline pH depends on MYB72-mediated repression of CYTOCHROME P450, FAMILY 82, SUBFAMILY C, POLYPEPTIDE 4 (CYP82C4). In vitro, only fraxetin and sideretin can reduce part of the Fe(III) that they mobilize. We demonstrate that coumarin-mediated Fe(III) reduction is critical under acidic conditions, as fraxetin and sideretin can complement the Fe(III)-chelate reductase mutant ferric reduction oxidase 2 (fro2), and disruption of coumarin biosynthesis in fro2 plants impairs Fe acquisition similar to in the Fe(II) uptake-deficient mutant iron-regulated transporter 1 (irt1). Disruption of sideretin biosynthesis in a fro2 cyp82C4-1 double mutant revealed that sideretin is the dominant chemical reductant that functions with FRO2 to mediate Fe(II) formation for root uptake. At alkaline pH, Fe(III) reduction by coumarins becomes almost negligible but fraxetin still sustains high Fe(III) mobilization, suggesting that its main function is to provide chelated Fe(III) for FRO2. Our study indicates that strategy-I plants link sideretin and fraxetin biosynthesis and secretion to external pH to recruit distinct coumarin chemical activities to maximize Fe acquisition according to prevailing soil pH conditions.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Compostos Férricos/metabolismo , Ferro/metabolismo , Cumarínicos/metabolismo , Compostos Ferrosos/metabolismo , Raízes de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas
2.
Rev Physiol Biochem Pharmacol ; 183: 157-176, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-32767122

RESUMO

The intracellular Ca2+ concentration is mainly controlled by Ca2+ channels. These channels form complexes with K+ channels, which function to amplify Ca2+ flux. In cancer cells, voltage-gated/voltage-dependent Ca2+ channels and non-voltage-gated/voltage-independent Ca2+ channels have been reported to interact with K+ channels such as Ca2+-activated K+ channels and voltage-gated K+ channels. These channels are activated by an increase in cytosolic Ca2+ concentration or by membrane depolarization, which induces membrane hyperpolarization, increasing the driving force for Ca2+ flux. These complexes, composed of K+ and Ca2+ channels, are regulated by several molecules including lipids (ether lipids and cholesterol), proteins (e.g. STIM), receptors (e.g. S1R/SIGMAR1), and peptides (e.g. LL-37) and can be targeted by monoclonal antibodies, making them novel targets for cancer research.


Assuntos
Neoplasias , Canais de Potássio de Abertura Dependente da Tensão da Membrana , Cálcio/metabolismo , Canais de Cálcio/metabolismo , Humanos , Lipídeos , Neoplasias/tratamento farmacológico , Potássio/metabolismo , Canais de Potássio/metabolismo
3.
Cell ; 133(2): 364-74, 2008 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-18423206

RESUMO

To fully understand animal transcription networks, it is essential to accurately measure the spatial and temporal expression patterns of transcription factors and their targets. We describe a registration technique that takes image-based data from hundreds of Drosophila blastoderm embryos, each costained for a reference gene and one of a set of genes of interest, and builds a model VirtualEmbryo. This model captures in a common framework the average expression patterns for many genes in spite of significant variation in morphology and expression between individual embryos. We establish the method's accuracy by showing that relationships between a pair of genes' expression inferred from the model are nearly identical to those measured in embryos costained for the pair. We present a VirtualEmbryo containing data for 95 genes at six time cohorts. We show that known gene-regulatory interactions can be automatically recovered from this data set and predict hundreds of new interactions.


Assuntos
Drosophila melanogaster/genética , Redes Reguladoras de Genes , Modelos Genéticos , Animais , Blastoderma , Drosophila melanogaster/metabolismo , Embrião não Mamífero/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Genes de Insetos
4.
Microsc Microanal ; 27(4): 804-814, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34353384

RESUMO

Phase-contrast transmission electron microscopy (TEM) is a powerful tool for imaging the local atomic structure of materials. TEM has been used heavily in studies of defect structures of two-dimensional materials such as monolayer graphene due to its high dose efficiency. However, phase-contrast imaging can produce complex nonlinear contrast, even for weakly scattering samples. It is, therefore, difficult to develop fully automated analysis routines for phase-contrast TEM studies using conventional image processing tools. For automated analysis of large sample regions of graphene, one of the key problems is segmentation between the structure of interest and unwanted structures such as surface contaminant layers. In this study, we compare the performance of a conventional Bragg filtering method with a deep learning routine based on the U-Net architecture. We show that the deep learning method is more general, simpler to apply in practice, and produces more accurate and robust results than the conventional algorithm. We provide easily adaptable source code for all results in this paper and discuss potential applications for deep learning in fully automated TEM image analysis.

5.
Biometals ; 33(6): 305-321, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33015746

RESUMO

Due to the low iron solubility in alkaline soils, plants have evolved different iron acquisition strategies, which are either based on ferric iron reduction (strategy I) or complexation by phytosiderophores (strategy II). Recently, a prominent role of coumarins for iron acquisition has been discovered, but details of the respective mechanism remain unclear. Since coumarins may act as iron-binding ligands but also as reductants, various reaction sequences are possible, resulting in different iron species and oxidized coumarins. In this context, it is often overlooked that oxidized coumarins are not just byproducts of iron(III) reduction, but may be actively involved in further steps of iron mobilization. In order to verify this active role of oxidized coumarins in Fe(hydr)oxide dissolution, we complemented iron dissolution data with data of single coumarins (esculetin, scopoletin, fraxetin) and their oxidation products, as a function of time, pH, and mineral (goethite, lepidocrocite). Our results demonstrate that there are four different routes for coumarin oxidation, leading to quinones, dimers, hydroxylated coumarins, demethylated coumarins, and combinations of these. The time-dependent species pattern differs with respect to mineral, pH, and coumarin molecule. Oxidized coumarins are often more reactive than the original coumarins, explaining unexpected iron mobilization by scopoletin, which is demethylated to esculetin. Also oxidative hydroxylation and dimerization increase the number of phenolic groups and yield new chelating properties. Several iron-species are identified for the three coumarins. Since oxidation reactions are initiated directly at mineral surfaces, they are often very effective-but this does not always result in more iron mobilization.


Assuntos
Cumarínicos/química , Compostos Férricos/química , Minerais/química , Concentração de Íons de Hidrogênio , Oxirredução , Solubilidade
6.
BMC Bioinformatics ; 18(Suppl 6): 236, 2017 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-28617218

RESUMO

BACKGROUND: There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indicators for neurological diseases require the in-depth analysis of neural activity data from ECoG. Such data is multi-scale and is of high spatio-temporal resolution. Comprehensive analysis of this data should be supported by interactive visual analysis methods that allow a scientist to understand functional patterns at varying levels of granularity and comprehend its time-varying behavior. RESULTS: We introduce a novel multi-scale visual analysis system, ECoG ClusterFlow, for the detailed exploration of ECoG data. Our system detects and visualizes dynamic high-level structures, such as communities, derived from the time-varying connectivity network. The system supports two major views: 1) an overview summarizing the evolution of clusters over time and 2) an electrode view using hierarchical glyph-based design to visualize the propagation of clusters in their spatial, anatomical context. We present case studies that were performed in collaboration with neuroscientists and neurosurgeons using simulated and recorded epileptic seizure data to demonstrate our system's effectiveness. CONCLUSION: ECoG ClusterFlow supports the comparison of spatio-temporal patterns for specific time intervals and allows a user to utilize various clustering algorithms. Neuroscientists can identify the site of seizure genesis and its spatial progression during various the stages of a seizure. Our system serves as a fast and powerful means for the generation of preliminary hypotheses that can be used as a basis for subsequent application of rigorous statistical methods, with the ultimate goal being the clinical treatment of epileptogenic zones.


Assuntos
Encéfalo , Biologia Computacional/métodos , Eletrocorticografia/métodos , Algoritmos , Encéfalo/diagnóstico por imagem , Encéfalo/fisiopatologia , Análise por Conglomerados , Epilepsia/fisiopatologia , Humanos , Software
7.
Biochim Biophys Acta ; 1848(10 Pt B): 2603-20, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25450343

RESUMO

Membrane lipid rafts are distinct plasma membrane nanodomains that are enriched with cholesterol, sphingolipids and gangliosides, with occasional presence of saturated fatty acids and phospholipids containing saturated acyl chains. It is well known that they organize receptors (such as Epithelial Growth Factor Receptor), ion channels and their downstream acting molecules to regulate intracellular signaling pathways. Among them are Ca2+ signaling pathways, which are modified in tumor cells and inhibited upon membrane raft disruption. In addition to protein components, lipids from rafts also contribute to the organization and function of Ca2+ signaling microdomains. This article aims to focus on the lipid raft KCa/ClCa/Ca2+ channel complexes that regulate Ca2+ and EGFR signaling in cancer cells, and discusses the potential modification of these complexes by lipids as a novel therapeutic approach in tumor development. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers.


Assuntos
Antineoplásicos/uso terapêutico , Cálcio/metabolismo , Regulação Neoplásica da Expressão Gênica , Lipídeos de Membrana/antagonistas & inibidores , Microdomínios da Membrana/efeitos dos fármacos , Neoplasias/tratamento farmacológico , Canais de Cálcio/genética , Canais de Cálcio/metabolismo , Canais de Cloreto/antagonistas & inibidores , Canais de Cloreto/genética , Canais de Cloreto/metabolismo , Receptores ErbB/antagonistas & inibidores , Receptores ErbB/genética , Receptores ErbB/metabolismo , Ácidos Graxos Ômega-3/uso terapêutico , Humanos , Isoenzimas/genética , Isoenzimas/metabolismo , Ácidos Linoleicos Conjugados/uso terapêutico , Lipídeos de Membrana/química , Lipídeos de Membrana/metabolismo , Microdomínios da Membrana/metabolismo , Microdomínios da Membrana/ultraestrutura , Neoplasias/genética , Neoplasias/metabolismo , Neoplasias/patologia , Canais de Potássio/genética , Canais de Potássio/metabolismo , Transdução de Sinais , Células Tumorais Cultivadas
8.
Anal Bioanal Chem ; 408(4): 1237-47, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26670772

RESUMO

Small sulfur-containing compounds are involved in several important biochemical processes, including-but not limited to-redox regulation and drug conjugation/detoxification. While methods for stable redox pairs of such compounds (thiols/disulfides) are available, analytical data on more labile and short-lived redox intermediates are scarce, due to highly challenging analytical requirements. In this study, we employ the direct combination of reagentless electrochemical oxidation and mass spectrometric (EC-MS) identification for monitoring oxidation reactions of cysteine, N-acetylcysteine, methionine, and glutathione under simulated physiological conditions (pH 7.4, 37 °C). For the first time, all theoretically expected redox intermediates-with only one exception-are detected simultaneously and in situ, including sulfenic, sulfinic, and sulfonic acids, disulfides, thiosulfinates, thiosulfonates, and sulfoxides. By monitoring the time/potential-dependent interconversion of sulfur species, mechanistic oxidation routes are confirmed and new reactions detected, e.g., sulfenamide formation due to reaction with ammonia from the buffer. Furthermore, our results demonstrate a highly significant impact of cisplatin on the redox reactivity of sulfur species. Namely, the amount of thiol oxidation to sulfonic acid via sulfenic and sulfinic acid intermediates is diminished for glutathione in the presence of cisplatin in favor of the disulfide formation, while for N-acetylcysteine the contrary applies. N-acetylcysteine is the only ligand which displays enhanced oxidation currents upon cisplatin addition, accompanied by increased levels of thiosulfinate and thiosulfonate species. This is traced back to thiol reactivity and highlights the important role of sulfenic acid intermediates, which may function as a switch between different oxidation routes.


Assuntos
Aminoácidos/química , Cisplatino/química , Eletroquímica/métodos , Glutationa/química , Espectrometria de Massas/métodos , Acetilcisteína/química , Cisplatino/metabolismo , Metionina/química , Oxirredução , Compostos de Sulfidrila/química , Compostos de Sulfidrila/metabolismo , Enxofre/química
9.
Biochemistry ; 54(17): 2785-98, 2015 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-25884905

RESUMO

Lung cysteine cathepsins B, K, L, and S contribute to physiological and pathological processes including degradation of antimicrobial peptides/proteins (AMPs) such as surfactant protein SP-A, lactoferrin, secretory leukocyte peptidase inhibitor, and beta-defensins-2 and -3. Substantial amounts of uncleaved LL-37, a 37-mer cationic AMP, were observed in the sputum of patients with cystic fibrosis (CF). Nevertheless LL-37 was degraded after prolonged incubation in CF sputum, and the hydrolysis was blocked by E-64, a selective inhibitor of cysteine proteases. Cathepsins K and S, expressed in human alveolar macrophages, thoroughly hydrolyzed LL-37 in vitro, whereas it competitively inhibited cathepsin L (Ki = 150 nM). Cleavage of LL-37 by cathepsins S and K impaired its antimicrobial activity against Pseudomonas aeruginosa and Staphylococcus aureus, in a time- and concentration-dependent manner. The exchange of residues 67 and 205 in the S2 pockets of cathepsins L (Leu67Tyr/Ala205Leu) and K (Tyr67Leu/Leu205Ala) switched the specificity of these mutants toward LL-37. Molecular modeling suggested that LL-37 interacted with the active site of cathepsin L in both forward (i.e., substrate-like) and reverse orientations with similar binding energies. Our data support the hypothesis that cysteine cathepsins modulate the innate immunity response by degrading distinct and representative members of the AMP family.


Assuntos
Peptídeos Catiônicos Antimicrobianos/metabolismo , Catepsina K/metabolismo , Catepsina L/antagonistas & inibidores , Catepsinas/metabolismo , Inibidores de Cisteína Proteinase/metabolismo , Sequência de Aminoácidos , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/farmacologia , Líquido da Lavagem Broncoalveolar , Dicroísmo Circular , Inibidores de Cisteína Proteinase/farmacologia , Fibrose Cística/microbiologia , Humanos , Macrófagos Alveolares/metabolismo , Testes de Sensibilidade Microbiana , Dados de Sequência Molecular , Pseudomonas aeruginosa/efeitos dos fármacos , Especificidade por Substrato , Catelicidinas
10.
Pflugers Arch ; 467(6): 1249-59, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25017107

RESUMO

Peroxisome proliferator-activated receptor ß (PPARß) and NaV1.5 voltage-gated sodium channels have independently been shown to regulate human breast cancer cell invasiveness. The n-3 polyunsaturated docosahexaenoic acid (DHA, 22:6n-3), a natural ligand of PPAR, is effective in increasing survival and chemotherapy efficacy in breast cancer patient with metastasis. DHA reduces breast cancer cell invasiveness and it also inhibits PPARß expression. We have shown previously that NaV1.5 promotes MDA-MB-231 breast cancer cells invasiveness by potentiating the activity of Na(+)/H(+) exchanger type 1 (NHE-1), the major regulator of H(+) efflux in these cells. We report here that DHA inhibited NaV1.5 current and NHE-1 activity in human breast cancer cells, and in turn reduced NaV1.5-dependent cancer cell invasiveness. For the first time, we show that antagonizing PPARß, or inhibiting its expression, reduced NaV1.5 mRNA and protein expression and NaV1.5 current, as well as NHE-1 activity and cell invasiveness. Consistent with these results, the DHA-induced reduction of both NaV1.5 expression and NHE-1 activity was abolished in cancer cells knocked-down for the expression of PPARß (shPPARß). This demonstrates a direct link between the inhibition of PPARß expression and the inhibition of Nav1.5/NHE-1 activities and breast cancer cell invasiveness. This study provides new mechanistic data advocating for the use of natural fatty acids such as DHA to block the development of breast cancer metastases.


Assuntos
Movimento Celular/efeitos dos fármacos , Ácidos Docosa-Hexaenoicos/farmacologia , Canal de Sódio Disparado por Voltagem NAV1.5/metabolismo , PPAR beta/metabolismo , Linhagem Celular Tumoral , Humanos , Canal de Sódio Disparado por Voltagem NAV1.5/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
11.
Electrophoresis ; 36(4): 509-17, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25483804

RESUMO

Pt-based anticancer drugs, such as cisplatin, are known to undergo several (bio-)chemical transformation steps after administration. Hydrolysis and adduct formation with small nucleophiles and larger proteins are their most relevant reactions on the way to the final reaction site (DNA), but there are still many open questions regarding the identity and pharmacological relevance of various proposed adducts and intermediates. Furthermore, the role of buffer components or additives, which are inevitably added to samples during any type of analytical measurement, has been frequently neglected in previous studies. Here, we report on adduct formation reactions of the fluorescent cisplatin analogue carboxyfluorescein diacetate platinum (CFDA-Pt) in commonly used buffers and cell culture medium. Our results indicate that chelation reactions with noninnocent buffers (e.g., Tris) and components of the cell culture/cell lysis medium must be taken into account when interpreting results. Adduct formation kinetics was followed up to 60 h at nanomolar concentrations of CFDA-Pt by using CE-LIF. CE-MS enabled the online identification of such unexpected adducts down to the nanomolar concentration range. By using an optimized sample preparation strategy, unwanted adducts can be avoided and several fluorescent adducts of CFDA-Pt are detectable in sensitive and cisplatin-resistant cancer cell lines. By processing samples rapidly after incubation, we could even identify the initial, but transient, Pt species in the cells as deacetylated CFDA-Pt with unaltered complexing environment at Pt. Overall, the proposed procedure enables a very sensitive and accurate analysis of low molecular mass Pt species in cancer cells, involving a fast CE-LIF detection within 5 min.


Assuntos
Cisplatino/análogos & derivados , Adutos de DNA/análise , Eletroforese Capilar/métodos , Fluoresceínas/análise , Antineoplásicos/análise , Antineoplásicos/química , Soluções Tampão , Linhagem Celular Tumoral/efeitos dos fármacos , Cisplatino/análise , Cisplatino/química , Eletroforese Capilar/instrumentação , Corantes Fluorescentes/análise , Corantes Fluorescentes/química , Humanos , Lasers Semicondutores , Peso Molecular , Espectrometria de Massas por Ionização por Electrospray
12.
IEEE Trans Vis Comput Graph ; 30(1): 1085-1094, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37871087

RESUMO

Over the last decade merge trees have been proven to support a plethora of visualization and analysis tasks since they effectively abstract complex datasets. This paper describes the ExTreeM-Algorithm: A scalable algorithm for the computation of merge trees via extremum graphs. The core idea of ExTreeM is to first derive the extremum graph G of an input scalar field f defined on a cell complex K, and subsequently compute the unaugmented merge tree of f on G instead of K; which are equivalent. Any merge tree algorithm can be carried out significantly faster on G, since K in general contains substantially more cells than G. To further speed up computation, ExTreeM includes a tailored procedure to derive merge trees of extremum graphs. The computation of the fully augmented merge tree, i.e., a merge tree domain segmentation of K, can then be performed in an optional post-processing step. All steps of ExTreeM consist of procedures with high parallel efficiency, and we provide a formal proof of its correctness. Our experiments, performed on publicly available datasets, report a speedup of up to one order of magnitude over the state-of-the-art algorithms included in the TTK and VTK-m software libraries, while also requiring significantly less memory and exhibiting excellent scaling behavior.

13.
Artigo em Alemão | MEDLINE | ID: mdl-23633250

RESUMO

The present work provides assistance for physicians concerning decision making in clinical borderline situations in the ICU. Based on a structured checklist the two fundamental aspects of any medical decision, the medical indication and the patient's preference are queried in a systematic way. Four possible steps of withholding and/or withdrawing therapy are discussed. Finally, recommendations regarding appropriate documentation of end of life decisions are provided.


Assuntos
Termos de Consentimento/ética , Cuidados Críticos/ética , Tomada de Decisões , Documentação/ética , Ordens quanto à Conduta (Ética Médica)/ética , Assistência Terminal/ética , Suspensão de Tratamento/ética , Alemanha , Humanos , Relações Médico-Paciente/ética , Terminologia como Assunto
14.
New Phytol ; 195(2): 372-383, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22591276

RESUMO

• Retranslocation of iron (Fe) from source leaves to sinks requires soluble Fe binding forms. As much of the Fe is protein-bound and associated with the leaf nitrogen (N) status, we investigated the role of N in Fe mobilization and retranslocation under N deficiency- vs dark-induced leaf senescence. • By excluding Fe retranslocation from the apoplastic root pool, Fe concentrations in source and sink leaves from hydroponically grown barley (Hordeum vulgare) plants were determined in parallel with the concentrations of potential Fe chelators and the expression of genes involved in phytosiderophore biosynthesis. • N supply showed opposing effects on Fe pools in source leaves, inhibiting Fe export out of source leaves under N sufficiency but stimulating Fe export from source leaves under N deficiency, which partially alleviated Fe deficiency-induced chlorosis. Both triggers of leaf senescence, shading and N deficiency, enhanced NICOTIANAMINE SYNTHASE2 gene expression, soluble Fe pools in source leaves, and phytosiderophore and citrate rather than nicotianamine concentrations. • These results indicate that Fe mobilization within senescing leaves is independent of a concomitant N sink in young leaves and that phytosiderophores enhance Fe solubility in senescing source leaves, favoring subsequent Fe retranslocation.


Assuntos
Hordeum/crescimento & desenvolvimento , Hordeum/metabolismo , Ferro/metabolismo , Folhas de Planta/metabolismo , Ácido Azetidinocarboxílico/análogos & derivados , Ácido Azetidinocarboxílico/metabolismo , Transporte Biológico/efeitos dos fármacos , Ácido Cítrico/metabolismo , Escuridão , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Hordeum/efeitos dos fármacos , Hordeum/genética , Nitrogênio/deficiência , Nitrogênio/metabolismo , Nitrogênio/farmacologia , Fenótipo , Folhas de Planta/efeitos dos fármacos , Folhas de Planta/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Solubilidade/efeitos dos fármacos
15.
IEEE Trans Vis Comput Graph ; 28(10): 3471-3485, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-33684039

RESUMO

Contour trees are used for topological data analysis in scientific visualization. While originally computed with serial algorithms, recent work has introduced a vector-parallel algorithm. However, this algorithm is relatively slow for fully augmented contour trees which are needed for many practical data analysis tasks. We therefore introduce a representation called the hyperstructure that enables efficient searches through the contour tree and use it to construct a fully augmented contour tree in data parallel, with performance on average 6 times faster than the state-of-the-art parallel algorithm in the TTK topological toolkit.


Assuntos
Gráficos por Computador , Algoritmos
16.
Electrophoresis ; 32(6-7): 772-81, 2011 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21192102

RESUMO

IEF is known as a powerful electrophoretic separation technique for amphoteric molecules, in particular for proteins. The objective of the present work is to prove the suitability of IEF also for the separation of small, non-covalent metal species. Investigations are performed with copper-glutathione complexes, with the synthetic ligand ethylenediamine-N,N'-bis(o-hydroxyphenyl)acetic acid (EDDHA) and respective metal complexes (Fe, Ga, Al, Ni, Zn), and with the phytosiderophore 2'-deoxymugineic acid (DMA) and its ferric complex. It is shown that ethylenediamine-N,N'-bis(o-hydroxyphenyl)acetic acid and DMA species are stable during preparative scale IEF, whereas copper-glutathione dissociates considerably. It is also shown that preparative scale IEF can be applied successfully to isolate ferric DMA from real plant samples, and that multidimensional separations are possible by combining preparative scale IEF with subsequent HPLC-MS analysis. Focusing of free ligands and respective metal complexes with di- and trivalent metals results in different pIs, but CIEF is usually needed for a reliable estimation of pI values. Limitations of the proposed methods (preparative IEF and CIEF) and consequences of the results with respect to metal speciation in plants are discussed.


Assuntos
Complexos de Coordenação/análise , Focalização Isoelétrica/métodos , Extratos Vegetais/química , Triticum/química , Cromatografia Líquida de Alta Pressão , Espectrometria de Massas
17.
IEEE Trans Vis Comput Graph ; 27(4): 2437-2454, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-31689193

RESUMO

As data sets grow to exascale, automated data analysis and visualization are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this form of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. We report the first shared SMP algorithm for fully parallel contour tree computation, with formal guarantees of O(lg V lg t) parallel steps and O(V lg V) work for data with V samples and t contour tree supernodes, and implementations with more than 30× parallel speed up on both CPU using TBB and GPU using Thrust and up 70× speed up compared to the serial sweep and merge algorithm.

18.
Cell Calcium ; 97: 102435, 2021 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-34167050

RESUMO

The Transient Receptor Potential Vanilloid type 2 (TRPV2) channel is highly selective for Ca2+ and can be activated by lipids, such as LysoPhosphatidylCholine (LPC). LPC analogues, such as the synthetic alkyl-ether-lipid edelfosine or the endogenous alkyl-ether-lipid Platelet Activating Factor (PAF), modulates ion channels in cancer cells. This opens the way to develop alkyl-ether-lipids for the modulation of TRPV2 in cancer. Here, we investigated the role of 2-Acetamido-2-Deoxy-l-O-Hexadecyl-rac-Glycero-3-PhosphatidylCholine (AD-HGPC), a new alkyl-ether-lipid (LPC analogue), on TRPV2 trafficking and its impact on Ca2+ -dependent cell migration. The effect of AD-HGPC on the TRPV2 channel and tumour process was further investigated using calcium imaging and an in vivo mouse model. Using molecular and pharmacological approaches, we dissected the mechanism implicated in alkyl-ether-lipids sensitive TRPV2 trafficking. We found that TRPV2 promotes constitutive Ca2+ entry, leading to migration of highly metastatic breast cancer cell lines through the PI3K/Akt-Girdin axis. AD-HGPC addresses the functional TRPV2 channel in the plasma membrane through Golgi stimulation and PI3K/Akt/Rac-dependent cytoskeletal reorganization, leading to constitutive Ca2+ entry and breast cancer cell migration (without affecting the development of metastasis), in a mouse model. We describe, for the first time, the biological role of a new alkyl-ether-lipid on TRPV2 channel trafficking in breast cancer cells and highlight the potential modulation of TRPV2 by alkyl-ether-lipids as a novel avenue for research in the treatment of metastatic cancer.

19.
Exp Dermatol ; 19(4): 332-8, 2010 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19878298

RESUMO

Cathelicidin antimicrobial protein, hCAP18, is the sole cathelin protein in human. Its C-terminal peptide, which is released enzymatically from the holoprotein, has broad antimicrobial activity but also has effects on eukaryotic cells. hCAP18 is present in leukocytes and is produced at epithelial interfaces as part of the innate immune system. In normal intact skin, there is low constitutive expression of hCAP18, which is rapidly upregulated upon injury. Accumulating evidence indicates that hCAP18/LL-37 may serve a key role in protecting the integrity of the epithelium and also actively promote re-epithelialization and tissue repair. Molecular mechanisms responsible for controlling hCAP18 gene expression in vivo are only partly understood. Vitamin D(3) and its analogue calcipotriol were recently found to directly induce transcription of the hCAP18 gene via functional vitamin D responsive elements in the hCAP18 gene promoter. Skin is the major source for vitamin D(3) in human, where its production is dependent on ultraviolet B (UVB) radiation. We have shown that exposure to UVB, sufficient to produce vitamin D(3), upregulates hCAP18 in human skin in vivo. In the present study, we demonstrate that the upregulation of hCAP18/LL-37 following acute skin injury is further enhanced, at both hCAP18 mRNA and protein levels, after topical treatment with the vitamin D(3) analogue calcipotriol. In chronic ulcers, calcipotriol treatment upregulated hCAP18 mRNA, whereas no consistent upregulation of hCAP18 protein was detected. Our results further support the role of vitamin D(3) as a key physiologic regulator of hCAP18/LL-37 in human skin.


Assuntos
Peptídeos Catiônicos Antimicrobianos/metabolismo , Calcitriol/análogos & derivados , Regulação para Cima/efeitos dos fármacos , Vitamina D/análogos & derivados , Ferimentos e Lesões/metabolismo , 25-Hidroxivitamina D3 1-alfa-Hidroxilase/genética , Administração Tópica , Adulto , Idoso , Idoso de 80 Anos ou mais , Peptídeos Catiônicos Antimicrobianos/genética , Calcitriol/administração & dosagem , Calcitriol/farmacologia , Calcitriol/uso terapêutico , Fármacos Dermatológicos/administração & dosagem , Fármacos Dermatológicos/farmacologia , Fármacos Dermatológicos/uso terapêutico , Feminino , Humanos , Úlcera da Perna/tratamento farmacológico , Úlcera da Perna/metabolismo , Masculino , Pessoa de Meia-Idade , Pele/efeitos dos fármacos , Pele/metabolismo , Regulação para Cima/genética , Cicatrização/efeitos dos fármacos , Cicatrização/fisiologia , Ferimentos e Lesões/tratamento farmacológico , Adulto Jovem , Catelicidinas
20.
IEEE Trans Vis Comput Graph ; 16(2): 248-60, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20075485

RESUMO

This paper presents topology-based methods to robustly extract, analyze, and track features defined as subsets of isosurfaces. First, we demonstrate how features identified by thresholding isosurfaces can be defined in terms of the Morse complex. Second, we present a specialized hierarchy that encodes the feature segmentation independent of the threshold while still providing a flexible multiresolution representation. Third, for a given parameter selection, we create detailed tracking graphs representing the complete evolution of all features in a combustion simulation over several hundred time steps. Finally, we discuss a user interface that correlates the tracking information with interactive rendering of the segmented isosurfaces enabling an in-depth analysis of the temporal behavior. We demonstrate our approach by analyzing three numerical simulations of lean hydrogen flames subject to different levels of turbulence. Due to their unstable nature, lean flames burn in cells separated by locally extinguished regions. The number, area, and evolution over time of these cells provide important insights into the impact of turbulence on the combustion process. Utilizing the hierarchy, we can perform an extensive parameter study without reprocessing the data for each set of parameters. The resulting statistics enable scientists to select appropriate parameters and provide insight into the sensitivity of the results with respect to the choice of parameters. Our method allows for the first time to quantitatively correlate the turbulence of the burning process with the distribution of burning regions, properly segmented and selected. In particular, our analysis shows that counterintuitively stronger turbulence leads to larger cell structures, which burn more intensely than expected. This behavior suggests that flames could be stabilized under much leaner conditions than previously anticipated.


Assuntos
Gráficos por Computador , Incêndios , Temperatura Alta , Hidrogênio/química , Armazenamento e Recuperação da Informação/métodos , Reologia/métodos , Interface Usuário-Computador , Simulação por Computador , Imageamento Tridimensional/métodos , Modelos Químicos
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