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971.
972.
LuTHy: a double‐readout bioluminescence‐based two‐hybrid technology for quantitative mapping of protein–protein interactions in mammalian cells
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Philipp Trepte Sabrina Kruse Simona Kostova Sheila Hoffmann Alexander Buntru Anne Tempelmeier Christopher Secker Lisa Diez Aline Schulz Konrad Klockmeier Martina Zenkner Sabrina Golusik Kirstin Rau Sigrid Schnoegl Craig C Garner Erich E Wanker 《Molecular systems biology》2018,14(7)
Information on protein–protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double‐readout bioluminescence‐based two‐hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence‐based co‐precipitation (LuC). The double‐readout procedure detects interactions with higher sensitivity than traditional single‐readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease‐causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult‐onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease‐causing missense mutations L115R and ?L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease‐associated mutations impair protein activity in biological systems. 相似文献
973.
Roseli Santos de Freitas Camila Mika Kamikawa Adriana Pardini Vicentini 《Revista iberoamericana de micología》2018,35(1):27-31
Background
Current methods for the production of Histoplasma capsulatum antigens are problematic in terms of standardization, specificity, stability, repeatability and reproducibility.Aims
In this study, we sought to optimize the methodology for producing H. capsulatum antigens, and to evaluate its applicability.Methods
Antigenic preparations obtained from 12 H. capsulatum isolates were evaluated by double immunodiffusion and immunoblotting assays against homologous and heterologous sera.Results
The evaluated and optimized protocol allowed a more stable production, as well as repeatable, reproducible, with shorter culture time and less costly. By double immunodiffusion and immunoblotting assays, the best pattern of reactivity was observed for antigens obtained with 33 days of culture from the isolates 200 and 406 against the M antigen and for the isolate 200 with 15 days against H antigen. The SDS-PAGE presented antigenic components of molecular masses between 17 and 119 kDa. The immunoblotting sensitivity was 95.5% and 100% with histoplasmosis sera from ill patients and sera from H. capsulatum infected but otherwise healthy patients, respectively, to the antigen derived from isolates 200 and 406.Conclusions
We suggest the employment of the antigen from isolate 200, with 15 or 30 days of culture, in the double immunodiffusion and immunoblotting assays due to its good ability to discriminate both sera from patients with histoplasmosis illness and histoplasmosis infection, in addition to its high specificity against heterologous sera. 相似文献974.
Ok‐Ryul Song Christophe J Queval Raffaella Iantomasi Vincent Delorme Sabrina Marion Romain Veyron‐Churlet Elisabeth Werkmeister Michka Popoff Isabelle Ricard Samuel Jouny Nathalie Deboosere Frank Lafont Alain Baulard Laurent Marsollier Eik Hoffmann Priscille Brodin 《EMBO reports》2018,19(1):29-42
The interaction of Mycobacterium tuberculosis (Mtb) with pulmonary epithelial cells is critical for early stages of bacillus colonization and during the progression of tuberculosis. Entry of Mtb into epithelial cells has been shown to depend on F‐actin polymerization, though the molecular mechanisms are still unclear. Here, we demonstrate that mycobacterial uptake into epithelial cells requires rearrangements of the actin cytoskeleton, which are regulated by ADP‐ribosylation factor 1 (Arf1) and phospholipase D1 (PLD1), and is dependent on the M3 muscarinic receptor (M3R). We show that this pathway is controlled by Arf GTPase‐activating protein 1 (ArfGAP1), as its silencing has an impact on actin cytoskeleton reorganization leading to uncontrolled uptake and replication of Mtb. Furthermore, we provide evidence that this pathway is critical for mycobacterial entry, while the cellular infection with other pathogens, such as Shigella flexneri and Yersinia pseudotuberculosis, is not affected. Altogether, these results reveal how cortical actin plays the role of a barrier to prevent mycobacterial entry into epithelial cells and indicate a novel role for ArfGAP1 as a restriction factor of host–pathogen interactions. 相似文献
975.
Contribution of crop model structure,parameters and climate projections to uncertainty in climate change impact assessments 总被引:2,自引:0,他引:2
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Fulu Tao Reimund P. Rötter Taru Palosuo Carlos Gregorio Hernández Díaz‐Ambrona M. Inés Mínguez Mikhail A. Semenov Kurt Christian Kersebaum Claas Nendel Xenia Specka Holger Hoffmann Frank Ewert Anaelle Dambreville Pierre Martre Lucía Rodríguez Margarita Ruiz‐Ramos Thomas Gaiser Jukka G. Höhn Tapio Salo Roberto Ferrise Marco Bindi Davide Cammarano Alan H. Schulman 《Global Change Biology》2018,24(3):1291-1307
Climate change impact assessments are plagued with uncertainties from many sources, such as climate projections or the inadequacies in structure and parameters of the impact model. Previous studies tried to account for the uncertainty from one or two of these. Here, we developed a triple‐ensemble probabilistic assessment using seven crop models, multiple sets of model parameters and eight contrasting climate projections together to comprehensively account for uncertainties from these three important sources. We demonstrated the approach in assessing climate change impact on barley growth and yield at Jokioinen, Finland in the Boreal climatic zone and Lleida, Spain in the Mediterranean climatic zone, for the 2050s. We further quantified and compared the contribution of crop model structure, crop model parameters and climate projections to the total variance of ensemble output using Analysis of Variance (ANOVA). Based on the triple‐ensemble probabilistic assessment, the median of simulated yield change was ?4% and +16%, and the probability of decreasing yield was 63% and 31% in the 2050s, at Jokioinen and Lleida, respectively, relative to 1981–2010. The contribution of crop model structure to the total variance of ensemble output was larger than that from downscaled climate projections and model parameters. The relative contribution of crop model parameters and downscaled climate projections to the total variance of ensemble output varied greatly among the seven crop models and between the two sites. The contribution of downscaled climate projections was on average larger than that of crop model parameters. This information on the uncertainty from different sources can be quite useful for model users to decide where to put the most effort when preparing or choosing models or parameters for impact analyses. We concluded that the triple‐ensemble probabilistic approach that accounts for the uncertainties from multiple important sources provide more comprehensive information for quantifying uncertainties in climate change impact assessments as compared to the conventional approaches that are deterministic or only account for the uncertainties from one or two of the uncertainty sources. 相似文献
976.
Xavier Arnan Alan N. Andersen Heloise Gibb Catherine L. Parr Nathan J. Sanders Robert R. Dunn Elena Angulo Fabricio B. Baccaro Tom R. Bishop Raphaël Boulay Cristina Castracani Xim Cerdá Israel Del Toro Thibaut Delsinne David A. Donoso Emilie K. Elten Tom M. Fayle Matthew C. Fitzpatrick Crisanto Gómez Donato A. Grasso Blair F. Grossman Benoit Guénard Nihara Gunawardene Brian Heterick Benjamin D. Hoffmann Milan Janda Clinton N. Jenkins Petr Klimes Lori Lach Thomas Laeger Maurice Leponce Andrea Lucky Jonathan Majer Sean Menke Dirk Mezger Alessandra Mori Jimmy Moses Thinandavha Caswell Munyai Omid Paknia Martin Pfeiffer Stacy M. Philpott Jorge L.P. Souza Melanie Tista Heraldo L. Vasconcelos Javier Retana 《Global Change Biology》2018,24(10):4614-4625
The relationship between levels of dominance and species richness is highly contentious, especially in ant communities. The dominance‐impoverishment rule states that high levels of dominance only occur in species‐poor communities, but there appear to be many cases of high levels of dominance in highly diverse communities. The extent to which dominant species limit local richness through competitive exclusion remains unclear, but such exclusion appears more apparent for non‐native rather than native dominant species. Here we perform the first global analysis of the relationship between behavioral dominance and species richness. We used data from 1,293 local assemblages of ground‐dwelling ants distributed across five continents to document the generality of the dominance‐impoverishment rule, and to identify the biotic and abiotic conditions under which it does and does not apply. We found that the behavioral dominance–diversity relationship varies greatly, and depends on whether dominant species are native or non‐native, whether dominance is considered as occurrence or relative abundance, and on variation in mean annual temperature. There were declines in diversity with increasing dominance in invaded communities, but diversity increased with increasing dominance in native communities. These patterns occur along the global temperature gradient. However, positive and negative relationships are strongest in the hottest sites. We also found that climate regulates the degree of behavioral dominance, but differently from how it shapes species richness. Our findings imply that, despite strong competitive interactions among ants, competitive exclusion is not a major driver of local richness in native ant communities. Although the dominance‐impoverishment rule applies to invaded communities, we propose an alternative dominance‐diversification rule for native communities. 相似文献
977.
Steven D. Allison Adriana L. Romero‐Olivares Ying Lu John W. Taylor Kathleen K. Treseder 《Global Change Biology》2018,24(7):2884-2897
The magnitude and direction of carbon cycle feedbacks under climate warming remain uncertain due to insufficient knowledge about the temperature sensitivities of soil microbial processes. Enzymatic rates could increase at higher temperatures, but this response could change over time if soil microbes adapt to warming. We used the Arrhenius relationship, biochemical transition state theory, and thermal physiology theory to predict the responses of extracellular enzyme Vmax and Km to temperature. Based on these concepts, we hypothesized that Vmax and Km would correlate positively with each other and show positive temperature sensitivities. For enzymes from warmer environments, we expected to find lower Vmax, Km, and Km temperature sensitivity but higher Vmax temperature sensitivity. We tested these hypotheses with isolates of the filamentous fungus Neurospora discreta collected from around the globe and with decomposing leaf litter from a warming experiment in Alaskan boreal forest. For Neurospora extracellular enzymes, Vmax Q10 ranged from 1.48 to 2.25, and Km Q10 ranged from 0.71 to 2.80. In agreement with theory, Vmax and Km were positively correlated for some enzymes, and Vmax declined under experimental warming in Alaskan litter. However, the temperature sensitivities of Vmax and Km did not vary as expected with warming. We also found no relationship between temperature sensitivity of Vmax or Km and mean annual temperature of the isolation site for Neurospora strains. Declining Vmax in the Alaskan warming treatment implies a short‐term negative feedback to climate change, but the Neurospora results suggest that climate‐driven changes in plant inputs and soil properties are important controls on enzyme kinetics in the long term. Our empirical data on enzyme Vmax, Km, and temperature sensitivities should be useful for parameterizing existing biogeochemical models, but they reveal a need to develop new theory on thermal adaptation mechanisms. 相似文献
978.
Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction
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Juliana Artier Flávia da Silva Zandonadi Flávia Maria de Souza Carvalho Bianca Alves Pauletti Adriana Franco Paes Leme Carolina Moretto Carnielli Heloisa Sobreiro Selistre‐de‐Araujo Maria Célia Bertolini Jesus Aparecido Ferro José Belasque Júnior Julio Cezar Franco de Oliveira Maria Teresa Marques Novo‐Mansur 《Molecular Plant Pathology》2018,19(1):143-157
Citrus canker is a plant disease caused by Gram‐negative bacteria from the genus Xanthomonas. The most virulent species is Xanthomonas citri ssp. citri (XAC), which attacks a wide range of citrus hosts. Differential proteomic analysis of the periplasm‐enriched fraction was performed for XAC cells grown in pathogenicity‐inducing (XAM‐M) and pathogenicity‐non‐inducing (nutrient broth) media using two‐dimensional electrophoresis combined with liquid chromatography‐tandem mass spectrometry. Amongst the 40 proteins identified, transglycosylase was detected in a highly abundant spot in XAC cells grown under inducing condition. Additional up‐regulated proteins related to cellular envelope metabolism included glucose‐1‐phosphate thymidylyltransferase, dTDP‐4‐dehydrorhamnose‐3,5‐epimerase and peptidyl‐prolyl cis–trans‐isomerase. Phosphoglucomutase and superoxide dismutase proteins, known to be involved in pathogenicity in other Xanthomonas species or organisms, were also detected. Western blot and quantitative real‐time polymerase chain reaction analyses for transglycosylase and superoxide dismutase confirmed that these proteins were up‐regulated under inducing condition, consistent with the proteomic results. Multiple spots for the 60‐kDa chaperonin and glyceraldehyde‐3‐phosphate dehydrogenase were identified, suggesting the presence of post‐translational modifications. We propose that substantial alterations in cellular envelope metabolism occur during the XAC infectious process, which are related to several aspects, from defence against reactive oxygen species to exopolysaccharide synthesis. Our results provide new candidates for virulence‐related proteins, whose abundance correlates with the induction of pathogenicity and virulence genes, such as hrpD6, hrpG, hrpB7, hpa1 and hrpX. The results present new potential targets against XAC to be investigated in further functional studies. 相似文献
979.
An approach based on the total‐species accumulation curve and higher taxon richness to estimate realistic upper limits in regional species richness
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Stanislao Bevilacqua Karl Inne Ugland Adriana Plicanti Danilo Scuderi Antonio Terlizzi 《Ecology and evolution》2018,8(1):405-415
Most of accumulation curves tend to underestimate species richness, as they do not consider spatial heterogeneity in species distribution, or are structured to provide lower bound estimates and limited extrapolations. The total‐species (T–S) curve allows extrapolations over large areas while taking into account spatial heterogeneity, making this estimator more prone to attempt upper bound estimates of regional species richness. However, the T–S curve may overestimate species richness due to (1) the mismatch among the spatial units used in the accumulation model and the actual units of variation in β‐diversity across the region, (2) small‐scale patchiness, and/or (3) patterns of rarity of species. We propose a new framework allowing the T–S curve to limit overestimation and give an application to a large dataset of marine mollusks spanning over 11 km2 of subtidal bottom (W Mediterranean). As accumulation patterns are closely related across the taxonomic hierarchy up to family level, improvements of the T–S curve leading to more realistic estimates of family richness, that is, not exceeding the maximum number of known families potentially present in the area, can be considered as conducive to more realistic estimates of species richness. Results on real data showed that improvements of the T–S curve to accounts for true variations in β‐diversity within the sampled areas, small‐scale patchiness, and rarity of families led to the most plausible richness when all aspects were considered in the model. Data on simulated communities indicated that in the presence of high heterogeneity, and when the proportion of rare species was not excessive (>2/3), the procedure led to almost unbiased estimates. Our findings highlighted the central role of variations in β‐diversity within the region when attempting to estimate species richness, providing a general framework exploiting the properties of the T–S curve and known family richness to estimate plausible upper bounds in γ‐diversity. 相似文献
980.
Thayana Conceição Barbosa Bruno Almeida Lopes Caroline Barbieri Blunck Marcela Braga Mansur Adriana Vanessa Santini Deyl Mariana Emerenciano Maria S. Pombo-de-Oliveira 《BMC medical genomics》2018,11(1):122