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John L. Darcy Sean O. I. Swift Gerald M. Cobian Geoffrey L. Zahn Brian A. Perry Anthony S. Amend 《Molecular ecology》2020,29(16):3102-3115
A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape‐scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities. 相似文献
165.
Lauren C. Ponisio Perry de Valpine Nicholas Michaud Daniel Turek 《Ecology and evolution》2020,10(5):2385-2416
Improved efficiency of Markov chain Monte Carlo facilitates all aspects of statistical analysis with Bayesian hierarchical models. Identifying strategies to improve MCMC performance is becoming increasingly crucial as the complexity of models, and the run times to fit them, increases. We evaluate different strategies for improving MCMC efficiency using the open‐source software NIMBLE (R package nimble) using common ecological models of species occurrence and abundance as examples. We ask how MCMC efficiency depends on model formulation, model size, data, and sampling strategy. For multiseason and/or multispecies occupancy models and for N‐mixture models, we compare the efficiency of sampling discrete latent states vs. integrating over them, including more vs. fewer hierarchical model components, and univariate vs. block‐sampling methods. We include the common MCMC tool JAGS in comparisons. For simple models, there is little practical difference between computational approaches. As model complexity increases, there are strong interactions between model formulation and sampling strategy on MCMC efficiency. There is no one‐size‐fits‐all best strategy, but rather problem‐specific best strategies related to model structure and type. In all but the simplest cases, NIMBLE's default or customized performance achieves much higher efficiency than JAGS. In the two most complex examples, NIMBLE was 10–12 times more efficient than JAGS. We find NIMBLE is a valuable tool for many ecologists utilizing Bayesian inference, particularly for complex models where JAGS is prohibitively slow. Our results highlight the need for more guidelines and customizable approaches to fit hierarchical models to ensure practitioners can make the most of occupancy and other hierarchical models. By implementing model‐generic MCMC procedures in open‐source software, including the NIMBLE extensions for integrating over latent states (implemented in the R package nimbleEcology), we have made progress toward this aim. 相似文献
166.
Perry A. Frey Adrian D. Hegeman Frank J. Ruzicka 《Critical reviews in biochemistry and molecular biology》2013,48(1):63-88
ABSTRACTThe radical S-adenosylmethionine (SAM) superfamily currently comprises more than 2800 proteins with the amino acid sequence motif CxxxCxxC unaccompanied by a fourth conserved cysteine. The charcteristic three-cysteine motif nucleates a [4Fe–4S] cluster, which binds SAM as a ligand to the unique Fe not ligated to a cysteine residue. The members participate in more than 40 distinct biochemical transformations, and most members have not been biochemically characterized. A handful of the members of this superfamily have been purified and at least partially characterized. Significant mechanistic and structural information is available for lysine 2,3-aminomutase, pyruvate formate-lyase, coproporphyrinogen III oxidase, and MoaA required for molybdopterin biosynthesis. Biochemical information is available for spore photoproduct lyase, anaerobic ribonucleotide reductase activation subunit, lipoyl synthase, and MiaB involved in methylthiolation of isopentenyladenine-37 in tRNA. The radical SAM enzymes biochemically characterized to date have in common the cleavage of the [4Fe–4S]1 + –SAM complex to [4Fe–4S]2 +–Met and the 5′ -deoxyadenosyl radical, which abstracts a hydrogen atom from the substrate to initiate a radical mechanism. 相似文献
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G. A. Perry J. D. Jackson T. L. McDonald D. A. Crouse J. G. Sharp 《Preparative biochemistry & biotechnology》2013,43(5):431-447
Recent increases in the ability to detect low levels of immunofluorescence have shown the need for highly purified primary immunoreagents. There are now reports of purification of monoclonal antibodies using HPLC with reverse phase columns. In this study we have utilized standard size exclusion HPLC to purify both biotinylated and non-biotinylated monoclonal antibodies from hybridoma culture supernatants. Results indicated that both biotinylated and non-biotinylated monoclonal antibodies retained their antigen binding capacity after purification, and were not different in this capacity from commercially available, affinity purified reagents. These findings indicate that size exclusion HPLC may be used in the purification of biologically active monoclonal antibodies, and suggest that this technique may be used in the large scale production of antibodies and their fragments, in antibody purification from ascites fluid, and in antisera quality control. 相似文献
169.
Nicole A. Hynson Vincent S. F. T. Merckx Brian A. Perry Kathleen K. Treseder 《Biological invasions》2013,15(11):2373-2385
Pine species have become invasive throughout the globe and threaten to replace native biota. The threat of pine invasion is particularly pressing in parts of the tropics where there are no native pines. The factors that govern pine invasion are not often well understood. However, key to pine survival is an obligate and mutualistic interaction with ectomycorrhizal fungi. Thus for pines to successfully invade new habitats compatible ectomycorrhizal fungi must already be present, or be co-introduced. The purpose of this study was to examine the community structure of non-native ectomycorrhizal fungi associated with pine invasions in the Hawaiian Islands. To accomplish this we executed a field and greenhouse study and used a molecular ecology approach to identify the fungi associating with invasive pines in Hawai‘i. We show that: (1) ectomycorrhizal fungal species richness in non-native pine plantations is far less than what is found in pine’s native range, (2) there was a significant decrease in average ectomycorrhizal fungal species richness as distance from pine plantations increased and, (3) Suillus species were the dominant fungi colonizing pines outside plantations. The keystone ectomycorrhizal fungal taxa responsible for pine establishment in Hawai‘i are within genera commonly associated with pine invasions throughout the globe. We surmise that these fungi share functional traits such as the ability for long-distance dispersal from plantations and host tree colonization via spore that lead to their success when introduced to new habitats. 相似文献
170.
Charles Reese Shanice Dyer Beth Perry Michael Bonner James Oates Ann Hofbauer William Sessa Pascal Bernatchez Richard P Visconti Jing Zhang Corey M Hatfield Richard M Silver Stanley Hoffman Elena Tourkina 《Respiratory research》2013,14(1):90