Novel Methods for Metagenomic Analysis

By sampling the genetic content of microbes at the nucleotide level, metagenomics has rapidly established itself as the standard in characterizing the taxonomic diversity and functional capacity of microbial populations throughout nature. The decreasing cost of sequencing technologies and the simultaneous increase of throughput per run has given scientists the ability to deeply sample highly diverse communities on a reasonable budget. The Human Microbiome Project is representative of the flood of sequence data that will arrive in the coming years. Despite these advancements, there remains the significant challenge of analyzing massive metagenomic datasets to make appropriate biological conclusions. This dissertation is a collection of novel methods developed for improved analysis of metagenomic data: (1) We begin with Figaro, a statistical algorithm that quickly and accurately infers and trims vector sequence from large Sanger-based read sets without prior knowledge of the vector used in library construction. (2) Next, we perform a rigorous evaluation of methodologies used to cluster environmental 16S rRNA sequences into species-level operational taxonomic units, and discover that many published studies utilize highly stringent parameters, resulting in overestimation of microbial diversity. (3) To assist in comparative metagenomics studies, we have created Metastats, a robust statistical methodology for comparing large-scale clinical datasets with up to thousands of subjects. Given a collection of annotated metagenomic features (e.g. taxa, COGs, or pathways), Metastats determines which features are differentially abundant between two populations. (4) Finally, we report on a new methodology that employs the generalized Lotka-Volterra model to infer microbe-microbe interactions from longitudinal 16S rRNA data. It is our hope that these methods will enhance standard metagenomic analysis techniques to provide better insight into the human microbiome and microbial communities throughout our world. To assist metagenomics researchers and those developing methods, all software described in this thesis is open-source and available online

Seasonal changes in metabolic rates in muskoxen following twenty- four hours of starvation

Timing of seasonal trends in post-prandial energy expenditure (EE) was measured in muskoxen (2 males and 1 female) given a standardized meal followed by a 24-26 h starvation during 10 months over the course of a year. EE was significantly lower in winter than summer. CH4 production (EctM) was reversed with winter highs and summer lows. Ratio of ECH4:EE indicates a change in dietary efficiency but this difference was not associated with a seasonal shift in RQ which was constant. The main increase in EE from winter to summer occurred between April and May and the summer to winter decrease between August and Septembet

The 1st Balloon Valvuloplasty: An Historical Note

Balloon valvuloplasty (BV) is currently the treatment of choice for pulmonic stenosis in humans and dogs. Before permission was obtained to attempt the 1st BV in a child in 1982, the safety and efficacy of the procedure were tested in 1980 in an English Bulldog with spontaneous pulmonic stenosis. A fatal outcome would have caused indefinite postponement of BV in human patients, a procedure that currently benefits over 25,000 patients a year worldwide. This article describes the initial test procedure and its fortunate outcome in spite of unrecognized coronary anomalies in the bulldog. A small balloon was used in the test procedure, and fatal disruption of the anomalous left coronary artery (CA) did not occur as it has in several bulldogs since that time

Transition metal catalysis for novel syntheses and applications of arylboronic acids and their derivatives

The research investigations presented herein are concerned with the syntheses and applications of arylboronic acids and their derivatives; with a particular focus on their accessibility or utility in certain of the most significant modern transition metal-catalysed reactions to involve organoborons. Chapter 1 provides an introduction to the field of organoboron chemistry, from its roots employing borane and related highly reactive derivatives for uncatalysed hydroboration of olefins and acetylenes, to the modern classes of organoboron reagents of the greatest significance to the related contemporary transition metal-catalysed methodologies. Furthermore particular emphasis is placed on the discussion of arylboronic acids, their synthesis, and application to transition metal catalysis as a result of their propensity to undergo useful transmetallation events. Chapter 2 details the use of a commercially available sulfonated monophosphine ligand in the rhodium-catalysed 1,2-addition reaction employing aryl aldehydes and arylboronic acids in aqueous media. The high and continued activity of the catalytic complex is demonstrated by it being successfully recycled five consecutive times in the arylation reaction of an aryl aldehyde; as well as being active for the arylations of more sterically demanding aryl methyl ketone substrates. Chapter 3 details the design and synthesis of a novel bench-stable azidomethylene substituted arylboronate ester. The reactivity of this compound and a related analogue in both the coppercatalysed azide alkyne cycloaddition reaction and the Suzuki coupling reaction are detailed, culminating in the proof-of-concept use of such versatile synthetic building blocks in the synthesis of a drug-substance derivative. Chapter 4 details alternative synthetic approaches to that used in Chapter 3 in order to access bifunctional azidomethylene substituted arylboronate esters. In particular the application of Miyaura borylation of arylhalides bearing benzylic azides is addressed as a means to rapidly access substrates which are otherwise shown to be incompatible with classical s-block synthetic intermediates.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Real-Time Detection of Optical Transients with RAPTOR

Fast variability of optical objects is an interesting though poorly explored subject in modern astronomy. Real-time data processing and identification of transient celestial events in the images is very important for such study as it allows rapid follow-up with more sensitive instruments. We discuss an approach which we have developed for the RAPTOR project, a pioneering closed-loop system combining real-time transient detection with rapid follow-up. RAPTOR's data processing pipeline is able to identify and localize an optical transient within seconds after the observation. The testing we performed so far have been confirming the effectiveness of our method for the optical transient detection. The software pipeline we have developed for RAPTOR can easily be applied to the data from other experiments.Comment: 10 pages, 7 figures, to appear in SPIE proceedings vol. 484

East Texas and Western Louisiana Coastal Erosion Study, Year 4

The following report summarizes the major accomplishments achieved by the Bureau of Economic Geology during the fourth year study (FY 94-95) of coastal erosion and wetlands loss along the southeastern Texas coast. The report covers activities between September 1, 1994, and August 31, 1995. Major accomplishments are reported for each work element and task identified in the 5-year work plan of the cooperative agreement. Documents summarizing the major accomplishments and containing the important data sets and scientific conclusions are included as Addenda 1-12.Bureau of Economic Geolog

East Texas and Western Louisiana Coastal Erosion Study, Year 2

The following report summarizes the major accomplishments achieved by the Bureau of Economic Geology during the second year of study of coastal erosion and wetlands loss along the southeastern Texas coast. The report covers activities between July 1, 1992, and June 30, 1993, and includes the activities for the eighth quarter of the project. Major accomplishments are reported for each work element and task identified in the cooperative agreement. Documents summarizing the major accomplishments and containing the important scientific conclusions are included as Addendums 1-8.Bureau of Economic Geolog

East Texas and Western Louisiana Coastal Erosion Study, Year 3

The following report summarizes the major accomplishments achieved by the Bureau of Economic Geology during the third year of study (FY 93-94) of coastal erosion and wetlands loss along the southeastern Texas coast. The report covers activities between July 1, 1993, and August 31, 1994. Major accomplishments are reported for each work element and task identified in the cooperative agreement. Documents summarizing the major accomplishments and containing the important scientific conclusions are included as Addenda 1-5.Bureau of Economic Geolog

Real-Time Decision Fusion for Multimodal Neural Prosthetic Devices

The field of neural prosthetics aims to develop prosthetic limbs with a brain-computer interface (BCI) through which neural activity is decoded into movements. A natural extension of current research is the incorporation of neural activity from multiple modalities to more accurately estimate the user's intent. The challenge remains how to appropriately combine this information in real-time for a neural prosthetic device., i.e., fusing predictions from several single-modality decoders to produce a more accurate device state estimate. We examine two algorithms for continuous variable decision fusion: the Kalman filter and artificial neural networks (ANNs). Using simulated cortical neural spike signals, we implemented several successful individual neural decoding algorithms, and tested the capabilities of each fusion method in the context of decoding 2-dimensional endpoint trajectories of a neural prosthetic arm. Extensively testing these methods on random trajectories, we find that on average both the Kalman filter and ANNs successfully fuse the individual decoder estimates to produce more accurate predictions.Our results reveal that a fusion-based approach has the potential to improve prediction accuracy over individual decoders of varying quality, and we hope that this work will encourage multimodal neural prosthetics experiments in the future