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941.
Daniel Evans-Yamamoto Franois D Rouleau Piyush Nanda Koji Makanae Yin Liu Philippe
C Desprs Hitoshi Matsuo Motoaki Seki Alexandre K Dub Diana Ascencio Nozomu Yachie Christian
R Landry 《Nucleic acids research》2022,50(9):e54
Barcode fusion genetics (BFG) utilizes deep sequencing to improve the throughput of protein–protein interaction (PPI) screening in pools. BFG has been implemented in Yeast two-hybrid (Y2H) screens (BFG-Y2H). While Y2H requires test protein pairs to localize in the nucleus for reporter reconstruction, dihydrofolate reductase protein-fragment complementation assay (DHFR-PCA) allows proteins to localize in broader subcellular contexts and proves to be largely orthogonal to Y2H. Here, we implemented BFG to DHFR-PCA (BFG-PCA). This plasmid-based system can leverage ORF collections across model organisms to perform comparative analysis, unlike the original DHFR-PCA that requires yeast genomic integration. The scalability and quality of BFG-PCA were demonstrated by screening human and yeast interactions for >11 000 bait-prey pairs. BFG-PCA showed high-sensitivity and high-specificity for capturing known interactions for both species. BFG-Y2H and BFG-PCA capture distinct sets of PPIs, which can partially be explained based on the domain orientation of the reporter tags. BFG-PCA is a high-throughput protein interaction technology to interrogate binary PPIs that exploits clone collections from any species of interest, expanding the scope of PPI assays. 相似文献
942.
Etimad Huwait Sanaa Almowallad Rehab Al-Massabi Salma Saddeek Kalamegam Gauthaman Alexandre Prola 《Current issues in molecular biology》2022,44(5):2153
Atherosclerosis is an important cause of cardiovascular disorders worldwide. Natural botanical drugs have attracted attention due to their antioxidant, anti-inflammatory, and antiatherogenic properties in the treatment of atherosclerosis. Punicalagin is the major bioactive component of pomegranate peel, and has been shown to have antioxidant, anti-inflammatory, antiviral, anti proliferation, and anticancer properties. To explore its antiatherogenic properties at a molecular level, we investigated the genome-wide expression changes that occur in differentiated THP1 cells following treatment with a non-toxic dose of punicalagin. We also conducted a molecular docking simulation study to identify the molecular targets of punicalagin. 相似文献
943.
Mariana Z. Mangeiro Rafael A. Nunes Jos O.L. Vieira Jr. Vicente Mussi-Dias Alexandre P. Viana Ricardo M. Souza 《Journal of nematology》2022,54(1)
For decades there have been anecdotal claims of synergistic interactions between plant-parasitic nematodes and soil-borne fungi causing decline of productivity of passion fruit (Passiflora edulis) orchards. An empirical confirmation of these disease complexes would impact disease management and plant breeding for resistance. To test those claims, we subjected passion fruit plants to single or concomitant parasitism by Meloidogyne javanica or M. incognita and Fusarium nirenbergiae or Neocosmospora sp. under controlled conditions. Non-inoculated plants served as control for the assays. The severity of shoot symptoms and variables related to plant growth, the extent of fungal lesions, and nematode reproduction were assessed to characterize the interactions. The shoot symptoms and effect on plant growth induced by the pathogens varied, but no synergy between the pathogens was observed. Moreover, the volume of tissue lesioned by the fungi was not affected by co-parasitism of the nematodes. Conversely, plant resistance to the nematodes was not affected by co-parasitism of the fungi. The interactions M. incognita-F. nirenbergiae, M. incognita-Neocosmospora sp., M. javanica-F. nirenbergiae, and M. javanica-Neocosmospora sp. were not synergistic as previously claimed, but instead neutral. 相似文献
944.
945.
Halby L Ryabinin VA Sinyakov AN Novopashina DS Venyaminova AG Grokhovsky SL Surovaya AN Gursky GV Boutorine AS 《Journal of biomolecular structure & dynamics》2007,25(1):61-76
Two hairpin hexa(N-methylpyrrole)carboxamide DNA minor groove binders (MGB) were linked together via their N-termini in head-to-head orientation. Complex formation between these bis-MGB conjugates and target DNA has been studied using DNase I footprinting, circular dichroism, thermal dissociation, and molecular modeling. DNase I footprint revealed binding of these conjugates to all the sites of 492 b.p. DNA fragment containing (A/T)(n)X(m)(A/T)(p) sequences, where n>3, p>3; m=1,2; X = A,T,G, or C. Binding affinity depended on the sequence context of the target. CD experiments and molecular modeling showed that oligo(N-methylpyrrole)carboxamide moieties in the complex form two short antiparallel hairpins rather than a long parallel head-to-head hairpin. Binding of bis-MGB also stabilized a target duplex thermodynamically. Sequence specificity of bis-MGB/DNA binding was validated using bis-conjugates of sequence-specific hairpin (N-methylpyrrole)/(N-methylimidazole) carboxamides. In order to increase the size of recognition sequence, the conjugates of bis-MGB with triplex-forming oligonucleotides (TFO) were synthesized and compared to TFO conjugated with single MGB hairpin unit. Bis-MGB-oligonucleotide conjugates also bind to two blocks of three and more A.T/T.A pairs similarly to bis-MGB alone, independently of the oligonucleotide moiety, but with lower affinity. However, the role of TFO in DNA recognition was demonstrated for mono-MGB-TFO conjugate where the binding was detected mainly in the area of the target sequence consisting of both MGB and TFO recognition sites. Basing on the molecular modeling, three-dimensional models of both target DNA/bis-MGB and target DNA/TFO-bis-MGB complexes were built, where bis-MGB forms two antiparallel hairpins. According to the second model, one MGB hairpin is in the minor groove of 5'-adjacent A/T sequence next to the triplex-forming region, whereas the other one occupies the minor groove of the TFO binding polypurine tract. All these data together give a key information for the construction of MGB-MGB and MGB-oligonucleotide conjugates possessing high specificity and affinity for the target double-stranded DNA. 相似文献
946.
Mercedes Bustamante Carmenza Robledo‐Abad Richard Harper Cheikh Mbow Nijavalli H. Ravindranat Frank Sperling Helmut Haberl Alexandre de Siqueira Pinto Pete Smith 《Global Change Biology》2014,20(10):3270-3290
The agriculture, forestry and other land use (AFOLU) sector is responsible for approximately 25% of anthropogenic GHG emissions mainly from deforestation and agricultural emissions from livestock, soil and nutrient management. Mitigation from the sector is thus extremely important in meeting emission reduction targets. The sector offers a variety of cost‐competitive mitigation options with most analyses indicating a decline in emissions largely due to decreasing deforestation rates. Sustainability criteria are needed to guide development and implementation of AFOLU mitigation measures with particular focus on multifunctional systems that allow the delivery of multiple services from land. It is striking that almost all of the positive and negative impacts, opportunities and barriers are context specific, precluding generic statements about which AFOLU mitigation measures have the greatest promise at a global scale. This finding underlines the importance of considering each mitigation strategy on a case‐by‐case basis, systemic effects when implementing mitigation options on the national scale, and suggests that policies need to be flexible enough to allow such assessments. National and international agricultural and forest (climate) policies have the potential to alter the opportunity costs of specific land uses in ways that increase opportunities or barriers for attaining climate change mitigation goals. Policies governing practices in agriculture and in forest conservation and management need to account for both effective mitigation and adaptation and can help to orient practices in agriculture and in forestry towards global sharing of innovative technologies for the efficient use of land resources. Different policy instruments, especially economic incentives and regulatory approaches, are currently being applied however, for its successful implementation it is critical to understand how land‐use decisions are made and how new social, political and economic forces in the future will influence this process. 相似文献
947.
Eric T. Hoke I. T. Sachs‐Quintana Matthew T. Lloyd Isaac Kauvar William R. Mateker Alexandre M. Nardes Craig H. Peters Nikos Kopidakis Michael D. McGehee 《Liver Transplantation》2012,2(11):1351-1357
Understanding the stability and degradation mechanisms of organic solar materials is critically important to achieving long device lifetimes. Here, an investigation of the photodegradation of polymer:fullerene blend films exposed to ambient conditions for a variety of polymer and fullerene derivative combinations is presented. Despite the wide range in polymer stabilities to photodegradation, the rate of irreversible polymer photobleaching in blend films is found to consistently and dramatically increase with decreasing electron affinity of the fullerene derivative. Furthermore, blends containing fullerenes with the smallest electron affinities photobleached at a faster rate than films of the pure polymer. These observations can be explained by a mechanism where both the polymer and fullerene donate photogenerated electrons to diatomic oxygen to form the superoxide radical anion which degrades the polymer. 相似文献
948.
Diguta CF Rousseaux S Weidmann S Bretin N Vincent B Guilloux-Benatier M Alexandre H 《FEMS microbiology letters》2010,313(1):81-87
The aim of this study was to develop a system for rapid and accurate real-time quantitative PCR (qPCR) identification and quantification of Botrytis cinerea, one of the major pathogens present on grapes. The intergenic spacer (IGS) region of the nuclear ribosomal DNA was used to specifically detect and quantify B. cinerea. A standard curve was established to quantify this fungus. The qPCR reaction was based on the simultaneous detection of a specific IGS sequence and also contained an internal amplification control to compensate for variations in DNA extraction and the various compounds from grapes that inhibit PCR. In these conditions, the assay had high efficiency (97%), and the limit of detection was estimated to be 6.3 pg DNA (corresponding to 540 spores). Our method was applied to assess the effects of various treatment strategies against Botrytis in the vineyard. Our qPCR assay proved to be rapid, selective and sensitive and may be used to monitor Botrytis infection in vineyards. 相似文献
949.
Methods to account for spatial autocorrelation in the analysis of species distributional data: a review 总被引:19,自引:1,他引:19
Carsten F. Dormann Jana M. McPherson Miguel B. Araújo Roger Bivand Janine Bolliger Gudrun Carl Richard G. Davies Alexandre Hirzel Walter Jetz W. Daniel Kissling Ingolf Kühn Ralf Ohlemüller Pedro R. Peres-Neto Björn Reineking Boris Schröder Frank M. Schurr Robert Wilson 《Ecography》2007,30(5):609-628
Species distributional or trait data based on range map (extent‐of‐occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix. 相似文献
950.