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Title
Computational Frameworks for Indel-Aware Evolutionary Analysis using Large-Scale Genomic Sequence Data
Creator
Wang, Wei
Date
2021
Collection
Electronic Theses & Dissertations
Description
With the development of sequencing techniques, genetic sequencing data has been extensively used in evolutionary studies.The phylogenetic reconstruction problem, which is the reconstruction of evolutionary history from biomolecular sequences, is a fundamental problem. The evolutionary relationship between organisms is often represented by phylogeny, which is a tree or network representation. The most widely-used approach for reconstructing phylogenies from sequencing data involves two phases:...
Show moreWith the development of sequencing techniques, genetic sequencing data has been extensively used in evolutionary studies.The phylogenetic reconstruction problem, which is the reconstruction of evolutionary history from biomolecular sequences, is a fundamental problem. The evolutionary relationship between organisms is often represented by phylogeny, which is a tree or network representation. The most widely-used approach for reconstructing phylogenies from sequencing data involves two phases: multiple sequence alignment and phylogenetic reconstruction from the aligned sequences. As the amount of biomolecular sequence data increases, it has become a major challenge to develop efficient and accurate computational methods for phylogenetic analyses of large-scale sequencing data. Due to the complexity of the phylogenetic reconstruction problem in modern phylogenetic studies, the traditional sequence-based phylogenetic analysis methods involve many over-simplified assumptions. In this thesis, we describe our contribution in relaxing some of these over-simplified assumptions in the phylogenetic analysis.Insertion and deletion events, referred to as indels, carry much phylogenetic information but are often ignored in the reconstruction process of phylogenies. We take into account the indel uncertainties in multiple phylogenetic analyses by applying resampling and re-estimation. Another over-simplified assumption that we contributed to is adopted by many commonly used non-parametric algorithms for the resampling of biomolecular sequences, all sites in an MSA are evolved independently and identically distributed (i.i.d). Many evolution events, such as recombination and hybridization, may produce intra-sequence and functional dependence in biomolecular sequences that violate this assumption. We introduce SERES, a resampling algorithm for biomolecular sequences that can produce resampled replicates that preserve the intra-sequence dependence. We describe the application of the SERES resampling and re-estimation approach to two classical problems: the multiple sequence alignment support estimation and recombination-aware local genealogical inference. We show that these two statistical inference problems greatly benefit from the indel-aware resampling and re-estimation approach and the reservation of intra-sequence dependence.A major drawback of SERES is that it requires parameters to ensure the synchronization of random walks on unaligned sequences.We introduce RAWR, a non-parametric resampling method designed for phylogenetic tree support estimation that does not require extra parameters. We show that the RAWR-based resampling and re-estimation method produces comparable or typically better performance than the traditional bootstrap approach on the phylogenetic tree support estimation problem. We further relax the commonly used assumption of phylogeny.Evolutionary history is usually considered as a tree structure. Evolutionary events that cause reticulated gene flow are ignored. Previous studies show that alignment uncertainty greatly impacts downstream tree inference and learning. However, there is little discussion about the impact of MSA uncertainties on the phylogenetic network reconstruction. We show evidence that the errors introduced in MSA estimation decrease the accuracy of the inferred phylogenetic network, and an indel-aware reconstruction method is needed for phylogenetic network analysis. In this dissertation, we introduce our contribution to phylogenetic estimation using biomolecular sequence data involving complex evolutionary histories, such as sequence insertion and deletion processes and non-tree-like evolution.
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Title
Nanotechnology applications for biomass pretreatment, functional material fabrication and surface modification
Creator
Wang, Wei
Date
2012
Collection
Electronic Theses & Dissertations
Description
Nanotechnology has gained its prosperity in the past two decades because of extensive contributions from interdisciplinary collaboration and a favorable interaction with practical applications. It covers a huge spectrum of applications. The dissertation hereby, in conjunction with the three research projects conducted by the author, will make contributions to nanotechnology applications in the following three topics: biomass pretreatment in biofuel production, functional material fabrication...
Show moreNanotechnology has gained its prosperity in the past two decades because of extensive contributions from interdisciplinary collaboration and a favorable interaction with practical applications. It covers a huge spectrum of applications. The dissertation hereby, in conjunction with the three research projects conducted by the author, will make contributions to nanotechnology applications in the following three topics: biomass pretreatment in biofuel production, functional material fabrication and surface modification.First, a fast and efficient nano-scale shear hybrid alkaline (NSHA) pretreatment method of lignocellulosic biomass was introduced. In this work, corn stover was pretreated in a modified Taylor-Couette reactor with sodium hydroxide at room temperature, with a two-minute retention time and a 12500 s-1 shear rate. Synergistic effects induced by the NSHA pretreatment disrupted the naturally-formed recalcitrance of biomass and generated nano-scale polysaccharide aggregates that are ready to be digested. After the pretreatment, results revealed major removals of hemicellulose and lignin, leaving an up to 82 % of cellulose content in the remaining solid. Compared with untreated corn stover, an approximately 4-fold increase in enzymatic cellulose conversion and a 5-fold increase in hemicellulose conversion were achieved. Second, a nano-deposition strategy was developed to enhance the energy absorption capacity of aluminum (Al) open-cell foams. The energy absorption capacity of open cell foams can be enhanced by a homogeneous thickening of the foam struts. However, the enhancement is compromised since an increase in the plateau stress without a reduction in densification strain cannot be achieved. To overcome that problem, a featured non-cyanide nano-crystalline copper electro-deposition system was setup for the coating of open-cell Al foam, and, the energy absorption capacity as a function of foam pore size and Cu coating thickness was investigated. An up to 3-time enhancement was achieved with a 60 m Cu coating on Al foams with an average strut thickness of 192 m. The compressive stress-strain response of the composite samples showed no significant reduction of the densification strain compared to the uncoated foams. With the same overall strut thickness, nano-reinforced foams had superior energy absorption capacity over plain foams, with almost a 2-time enhancement.Finally, a facile "dip & rinse" method for nickel (Ni) electroless deposition on hydrophobic polymer surfaces was developed. The electroless deposition (metallization) usually incorporates a harsh and/or toxic surface conditioning to activate the substrate. To eliminate the need for that step, a facile method of electroless Ni deposition on various hydrophobic polymer substrates was demonstrated, by making use of the hydrophobic interactions between Poly(allylamine hydrochloride) (PAH) and polymer substrates for catalyst adsorption/immobilization. Various hydrophobic polymer surfaces with different geometries and dimensions, including low density polyethylene (LDPE), high density polyethylene (HDPE), polypropylene (PP) and polystyrene (PS) thin sheets, and PE pellets were tested and Ni was successfully deposited onto all these surfaces. A kinetic study on polymer thin sheets examples showed that with 2 hours of deposition, an approximately 2 m thickness was achieved. A prove-of-concept study showed that Ni coated polymer thin sheets can be further electrodeposited with heterogeneous metal (Cu), hence enabling a faster thickness growth over time.
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Title
Elastic and thermal properties of particulate composites with inhomogeneous interphases
Creator
Wang, Wei
Date
1994
Collection
Electronic Theses & Dissertations
Title
Entropy zero system and Morse-Smale systems
Creator
Wang, Wei
Date
1997
Collection
Electronic Theses & Dissertations
Title
Investigating soil aggregate pore structures and their relationship to bacteria spatial distribution using x-ray computed microtomography
Creator
Wang, Wei
Date
2012
Collection
Electronic Theses & Dissertations
Description
Soils are among the extremely complicated materials with intricate internal pore geometries. Soil's hierarchical structures control various physical, chemical and biological processes at different scales. At soil aggregate scale, configuration of pore space plays an important role in determining carbon (C) sequestration, water and gas flow as well as bacteria survival and transport. Understanding the complex interaction between soil aggregate structure and these processes will greatly help us...
Show moreSoils are among the extremely complicated materials with intricate internal pore geometries. Soil's hierarchical structures control various physical, chemical and biological processes at different scales. At soil aggregate scale, configuration of pore space plays an important role in determining carbon (C) sequestration, water and gas flow as well as bacteria survival and transport. Understanding the complex interaction between soil aggregate structure and these processes will greatly help us appreciate critical processes at larger scale. However, due to technical limitations on accessing aggregate interiors, it remained relatively poorly understood until recent advances of X-ray computed microtomography (μCT) imaging in soils. Overall, the dissertation aims to effectively utilize soil aggregate μCT imaging, to understand soil aggregate structure difference under contrasting land use and managements, and to investigate bacteria redistribution and transport pattern and its relation to aggregate pore characteristics.Synchrotron μCT provides a noninvasive approach to record three dimension (3D) information on soil aggregates with resolution of one to several microns. Image segmentation is the first step in μCT image analysis, however, lack of ground-truth images poses great challenge to soil image segmentation. Proposed simulation method successfully generated soil aggregate grey scale images from pore/solid binary images, thus provided ground-truth information. Indicator Kriging method was found preferable to other methods in this study when the image histogram is clearly bimodal. Region non-uniformity measure performs sufficiently well as a segmentation criterion. The second technical difficulty involves 3D soil aggregate boundary delineation. Image closing technique is a promising tool for boundary detection, yet it requires selecting optimal neighborhood parameter (r) so that aggregate exteriors can be properly defined - inclusion of all surface pores while keeping the surface sufficiently irregular. Examining the plots of the total aggregate volume, aggregate boundary fractal dimension against r could serve as useful criteria for selecting the optimal r value. After addressing these image processing issues, soil aggregates from long term contrasting soil types and land use practices were compared. Soil aggregate samples were from LTER site at Kellogg Biological Station, USA and CERN site at Shenyang, China. The studied soil managements are conventional tillage (CT), native succession vegetation (NS), and bare soil with no vegetation (BS). Significantly greater percent of pores > 15 μm in LTER-CT aggregates was observed as compared to those of LTER-NS. LTER-NS aggregates had more large pores (> 90 μm) than LTER-CT aggregates, while more medium sized pores (45-90 μm) were found in LTER-CT aggregates. Pores were larger in the aggregate interiors than in the exterior layers; while intermediate pores (45-90 μm) were more abundant in the aggregate exterior layers. This trend was present in all land use and management treatments of the study and was most pronounced in LTER-NS. These results implied that a general mechanism maybe responsible for aggregates formation, but long term land use could alter the magnitude and intensity of involved soil processes.The last part of the dissertation addressed E.coli redistribution and transport in soil aggregates. The studied soil aggregates were from LTER site with conventional tillage (CT), native succession vegetation (NS), and no-till (NT). E.coli redistribution within soil aggregates display a significant different spatial distribution pattern under air-dry and saturated flow condition. When E.coli was first applied to an air-dry aggregate, its resulting spatial distribution was highly heterogeneous in aggregates of all management practices. After saturation, equilibration, and water extraction the E.coli redistributed within the aggregate primarily in vertical direction and became more homogeneously spread. Only relatively small percent of E.coli has completely left the aggregates. Redistribution was most pronounced in CT aggregates, followed by NT, and was almost negligible in NS aggregates. E.coli spatial distribution was related to intra-aggregate pore characteristics; however, because of high variability of the intra-aggregate pores the relationships were weak.
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