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Search Results: 1 - 10 of 149038 matches for " Douglas W. Yu "
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Enhanced Structural Complexity Index: An Improved Index for Describing Forest Structural Complexity  [PDF]
Philip Becksch?fer, Philip Mundhenk, Christoph Kleinn, Yinqiu Ji, Douglas W. Yu, Rhett D. Harrison
Open Journal of Forestry (OJF) , 2013, DOI: 10.4236/ojf.2013.31005
Abstract:

The horizontal distribution of stems, stand density and the differentiation of tree dimensions are among the most important aspects of stand structure. An increasing complexity of stand structure is often linked to a higher number of species and to greater ecological stability. For quantification, the Structural Complexity Index (SCI) describes structural complexity by means of an area ratio of the surface that is generated by connecting the tree tops of neighbouring trees to form triangles to the surface that is covered by all triangles if projected on a flat plane. Here, we propose two ecologically relevant modifications of the SCI: The degree of mingling of tree attributes, quantified by a vector ruggedness measure, and a stem density term. We investigate how these two modifications influence index values. Data come from forest inventory field plots sampled along a disturbance gradient from heavily disturbed shrub land, through secondary regrowth to mature montane rainforest stands in Mengsong, Xishuangbanna,Yunnan,China. An application is described linking structural complexity, as described by the SCI and its modified versions, to changes in species composition of insect communities. The results of this study show that the Enhanced Structural Complexity Index (ESCI) can serve as a valuable tool for forest managers and ecologists for describing the structural complexity of forest stands and is particularly valuable for natural forests with a high degree of structural

Evaluating Southern Appalachian Forest Dynamics without Eastern Hemlock: Consequences of Herbivory by the Hemlock Woolly Adelgid  [PDF]
Andrew G. Birt, Yu Zeng, Maria D. Tchakerian, Robert N. Coulson, Charles W. Lafon, David M. Cairns, John Waldron, Weimin Xi, Szu-Hung Chen, Douglas A. Street
Open Journal of Forestry (OJF) , 2014, DOI: 10.4236/ojf.2014.42014
Abstract:

Eastern hemlock (Tsuga canadensis Carriére) and the Carolina hemlock (Tsuga caroliniana Engelmann) are ecologically important tree species in eastern North America forests that are currently threatened by the hemlock woolly adelgid (HWA, Adelges tsugae Annand, Hemiptera: Adelgidae). HWA has spread rapidly from its original introduction site into new areas. Once present, HWA kills its hosts over a period of 4 to 10 years leading to a phenomenon that is known scientifically and colloquially as hemlock decline. To date, quarantine, chemical management, and biocontrol efforts have failed to curb the spread of the HWA. As such, forest management efforts are now being redirected towards developing an understanding of the effects of hemlock removal on vegetation dynamics, changes in forest composition, and changes in ecosystem function. In this study, we parameterize a spatially explicit landscape simulation model LANDIS II for a specific forested region of the southern Appalachians. Parameterization involves defining the life-history attributes of 37 tree species occupying 11 ecological zones and is based on knowledge of: current vegetation composition data, recent historic management and fire regimes, and life-history traits of each species. The parameterized model is used to explore a simple scenario of catastrophic hemlock mortality likely to occur as a result of HWA herbivory. Our results emphasize that hemlock is an important foundation species. When hemlock is removed from the system, forest composition changes considerably with a greater presence of shade intolerant pine and oak species. Additionally, hemlock removal leads to a period of transient, relatively unstable

Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity
ChenXue Yang,YingQiu Ji,XiaoYang Wang,ChunYang Yang,Douglas W. Yu
Science China Life Sciences , 2013, DOI: 10.1007/s11427-012-4423-7
Abstract: A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons (‘metabarcoding’) have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.
The Type II Hsp40 Sis1 Cooperates with Hsp70 and the E3 Ligase Ubr1 to Promote Degradation of Terminally Misfolded Cytosolic Protein
Daniel W. Summers, Katie J. Wolfe, Hong Yu Ren, Douglas M. Cyr
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0052099
Abstract: Mechanisms for cooperation between the cytosolic Hsp70 system and the ubiquitin proteasome system during protein triage are not clear. Herein, we identify new mechanisms for selection of misfolded cytosolic proteins for degradation via defining functional interactions between specific cytosolic Hsp70/Hsp40 pairs and quality control ubiquitin ligases. These studies revolved around the use of S. cerevisiae to elucidate the degradation pathway of a terminally misfolded reporter protein, short-lived GFP (slGFP). The Type I Hsp40 Ydj1 acts with Hsp70 to suppress slGFP aggregation. In contrast, the Type II Hsp40 Sis1 is required for proteasomal degradation of slGFP. Sis1 and Hsp70 operate sequentially with the quality control E3 ubiquitin ligase Ubr1 to target slGFP for degradation. Compromise of Sis1 or Ubr1 function leads slGFP to accumulate in a Triton X-100-soluble state with slGFP degradation intermediates being concentrated into perinuclear and peripheral puncta. Interestingly, when Sis1 activity is low the slGFP that is concentrated into puncta can be liberated from puncta and subsequently degraded. Conversely, in the absence of Ubr1, slGFP and the puncta that contain slGFP are relatively stable. Ubr1 mediates proteasomal degradation of slGFP that is released from cytosolic protein handling centers. Pathways for proteasomal degradation of misfolded cytosolic proteins involve functional interplay between Type II Hsp40/Hsp70 chaperone pairs, PQC E3 ligases, and storage depots for misfolded proteins.
PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation
Ricardo Ramirez-Gonzalez, Douglas W. Yu, Catharine Bruce, Darren Heavens, Mario Caccamo, Brent C. Emerson
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057615
Abstract: High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5′ region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.
SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph
Chengxi Ye,Zhanshan Sam Ma,Charles H. Cannon,Mihai Pop,Douglas W. Yu
Computer Science , 2011,
Abstract: de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which scales with k-mer length and total diversity (N) of unique k-mers in the genome expressed in base pairs or roughly (2k+8)N bits. This limitation is particularly important with large-scale genome analysis and for sequencing centers that simultaneously process multiple genomes. We present a sparse de Bruijn graph structure, based on which we developed SparseAssembler that greatly reduces memory space requirements. The structure also allows us to introduce a novel method for the removal of substitution errors introduced during sequencing. The sparse de Bruijn graph structure skips g intermediate k-mers, therefore reducing the theoretical memory space requirement to ~(2k/g+8)N. We have found that a practical value of g=16 consumes approximately 10% of the memory required by standard de Bruijn graph-based algorithms but yields comparable results. A high error rate could potentially derail the SparseAssembler. Therefore, we developed a sparse de Bruijn graph-based denoising algorithm that can remove more than 99% of substitution errors from datasets with a \leq 2% error rate. Given that substitution error rates for the current generation of sequencers is lower than 1%, our denoising procedure is sufficiently effective to safeguard the performance of our algorithm. Finally, we also introduce a novel Dijkstra-like breadth-first search algorithm for the sparse de Bruijn graph structure to circumvent residual errors and resolve polymorphisms.
SparseAssembler2: Sparse k-mer Graph for Memory Efficient Genome Assembly
Chengxi Ye,Charles H. Cannon,Zhanshan Sam Ma,Douglas W. Yu,Mihai Pop
Computer Science , 2011,
Abstract: The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based algorithms, upon which some of the most widely used de novo genome assemblers have been built, we released SparseAssembler1. SparseAssembler1 can save as much as 90% memory consumption in comparison with the state-of-art assemblers, but it requires rounds of denoising to accurately assemble genomes. In this paper, we introduce a new general model for genome assembly that uses only sparse k-mers. The new model replaces the idea of the de Bruijn graph from the beginning, and achieves similar memory efficiency and much better robustness compared with our previous SparseAssembler1. Results: We demonstrate that the decomposition of reads of all overlapping k-mers, which is used in existing de Bruijn graph genome assemblers, is overly cautious. We introduce a sparse k-mer graph structure for saving sparse k-mers, which greatly reduces memory space requirements necessary for de novo genome assembly. In contrast with the de Bruijn graph approach, we devise a simple but powerful strategy, i.e., finding links between the k-mers in the genome and traversing following the links, which can be done by saving only a few k-mers. To implement the strategy, we need to only select some k-mers that may not even be overlapping ones, and build the links between these k-mers indicated by the reads. We can traverse through this sparse k-mer graph to build the contigs, and ultimately complete the genome assembly. Since the new sparse k-mers graph shares almost all advantages of de Bruijn graph, we are able to adapt a Dijkstra-like breadth-first search algorithm to circumvent sequencing errors and resolve polymorphisms.
基于18SrDNA的metabarcoading技术分析土壤小型动物多样性3种方法的比较
杨晨雪, 季吟秋, 王晓阳, 杨春燕, Yu Douglas W.
中国科学 生命科学 , 2012,
Abstract: 生态和环境管理方面的很多基本问题都需要涉及土壤及腐殖质小型动物多样性的特征描述.当前利用高通量测序技术获得条形码基因扩增子序列的方法(‘metabarcoding’)在生物多样性调查方面提供了高效有力的方法.然而,这一技术的广泛应用面临很大阻碍,即需要从大量原始序列数据中通过生物信息学方法处理获得很多候选基因.于是,我们比较了3个针对从固体基质中获得的18SrDNAmetabarcode数据的信息学处理方法:(ⅰ)USEARCH/CROP,(ⅱ)Denoiser/UCLUST以及(ⅲ)OCTUPUS.令人满意的是,这3个信息学处理方法得到了相似且与环境样本中已知特征分类单元高度相关的群落组成.然而,OCTUPUS由于过高的序列噪音出现了过度估计系统发育多样性的问题.因此,推荐USEARCH/CROP或Denoiser/UCLUST方法,二者均可在QIIME环境下运行.
A Role for Parasites in Stabilising the Fig-Pollinator Mutualism
Derek W. Dunn,Simon T. Segar,Jo Ridley,Ruth Chan,Ross H. Crozier,Douglas W. Yu,James M. Cook
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0060059
Abstract: Mutualisms are interspecific interactions in which both players benefit. Explaining their maintenance is problematic, because cheaters should outcompete cooperative conspecifics, leading to mutualism instability. Monoecious figs (Ficus) are pollinated by host-specific wasps (Agaonidae), whose larvae gall ovules in their “fruits” (syconia). Female pollinating wasps oviposit directly into Ficus ovules from inside the receptive syconium. Across Ficus species, there is a widely documented segregation of pollinator galls in inner ovules and seeds in outer ovules. This pattern suggests that wasps avoid, or are prevented from ovipositing into, outer ovules, and this results in mutualism stability. However, the mechanisms preventing wasps from exploiting outer ovules remain unknown. We report that in Ficus rubiginosa, offspring in outer ovules are vulnerable to attack by parasitic wasps that oviposit from outside the syconium. Parasitism risk decreases towards the centre of the syconium, where inner ovules provide enemy-free space for pollinator offspring. We suggest that the resulting gradient in offspring viability is likely to contribute to selection on pollinators to avoid outer ovules, and by forcing wasps to focus on a subset of ovules, reduces their galling rates. This previously unidentified mechanism may therefore contribute to mutualism persistence independent of additional factors that invoke plant defences against pollinator oviposition, or physiological constraints on pollinators that prevent oviposition in all available ovules.
A Role for Parasites in Stabilising the Fig-Pollinator Mutualism
Derek W Dunn,Simon T Segar,Jo Ridley,Ruth Chan,Ross H Crozier,Douglas W Yu,James M Cook
PLOS Biology , 2008, DOI: 10.1371/journal.pbio.0060059
Abstract: Mutualisms are interspecific interactions in which both players benefit. Explaining their maintenance is problematic, because cheaters should outcompete cooperative conspecifics, leading to mutualism instability. Monoecious figs (Ficus) are pollinated by host-specific wasps (Agaonidae), whose larvae gall ovules in their “fruits” (syconia). Female pollinating wasps oviposit directly into Ficus ovules from inside the receptive syconium. Across Ficus species, there is a widely documented segregation of pollinator galls in inner ovules and seeds in outer ovules. This pattern suggests that wasps avoid, or are prevented from ovipositing into, outer ovules, and this results in mutualism stability. However, the mechanisms preventing wasps from exploiting outer ovules remain unknown. We report that in Ficus rubiginosa, offspring in outer ovules are vulnerable to attack by parasitic wasps that oviposit from outside the syconium. Parasitism risk decreases towards the centre of the syconium, where inner ovules provide enemy-free space for pollinator offspring. We suggest that the resulting gradient in offspring viability is likely to contribute to selection on pollinators to avoid outer ovules, and by forcing wasps to focus on a subset of ovules, reduces their galling rates. This previously unidentified mechanism may therefore contribute to mutualism persistence independent of additional factors that invoke plant defences against pollinator oviposition, or physiological constraints on pollinators that prevent oviposition in all available ovules.
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