Life Sciences Commons^™

Mechanism Of Lignin Inhibition Of Enzymatic Biomass Deconstruction, Josh V. Vermaas, Loukas Petridis, Xianghong Qi, Roland Schulz, Benjamin Lindner, Jeremy C. Smith

Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology

Background

The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process.

Results

By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are …

How Chip Size Impacts Steam Pretreatment Effectiveness For Biological Conversion Of Poplar Wood Into Fermentable Sugars, Jaclyn D. Demartini, Marcus Foston, Xianzhi Meng, Seokwon Jung, Rajeev Kumar, Arthur J. Ragauskas, Charles E. Wyman

Faculty Publications and Other Works -- Chemical and Biomolecular Engineering

Background

Woody biomass is highly recalcitrant to enzymatic sugar release and often requires significant size reduction and severe pretreatments to achieve economically viable sugar yields in biological production of sustainable fuels and chemicals. However, because mechanical size reduction of woody biomass can consume significant amounts of energy, it is desirable to minimize size reduction and instead pretreat larger wood chips prior to biological conversion. To date, however, most laboratory research has been performed on materials that are significantly smaller than applicable in a commercial setting. As a result, there is a limited understanding of the effects that larger biomass particle …

Assessment Of Genetic Diversity And Hybridization For The Endangered Conasauga Logperch (Percina Jenkinsi), Gregory R. Moyer, Anna L. George, Patrick L. Rakes, J.R. Shute, Ashantye' S. Williams

Southeastern Fishes Council Proceedings

The Conasauga logperch, Percina jenkinsi is one of the rarest darters in North America afforded protection under the Endangered Species Act. Unfortunately, little is known about potential threats to the genetic diversity of this species, a narrow endemic. Loss of genetic diversity, spawning of closely related individuals, and hybridization with closely related congeners have been known to increase the rate of extinction for threatened or endangered taxa. We evaluated these risks by estimating and comparing levels of genetic diversity between P. jenkinsi and P. kathae (a closely related, morphologically similar, and more abundant congener) using twelve microsatellite loci. Specifically, we …

Physiological Characterization Of Prochlorococcus Under Abiotic Stressors Temperature And Hydrogen Peroxide, Lanying Ma

Doctoral Dissertations

Cyanobacteria of the genus Prochlorococcus are the smallest and most abundant phytoplankters in the ocean. Temperature is a major influence on Prochlorococcus abundance and distribution in the ocean, but the physiological basis for this relationship is not well understood. In other microbes, lipid and fatty acid composition have been shown to be influenced by temperature, and temperature has also been proposed as a relevant factor for setting the elemental allocation in marine phytoplankton. In this study, we found that percentage of fatty acids unsaturation was negatively related with temperature in some Prochlorococcus strains, but this was not universal. Temperature had …

Health Assessment Of Two Reintroduced Populations Of American Martens (Martes Americana) In Michigan, Maria Catherine Spriggs

Doctoral Dissertations

The American marten (Martes americana) was extirpated from Michigan during the early-20th century due to loss of vast areas of mature conifer forest and unregulated trapping. The species was reintroduced into the Upper Peninsula (UP) and Northern Lower Peninsula (NLP) during the mid-20th century. While the American marten population in the UP has grown and is doing well, the population in the NLP has been less successful. The reasons for the limited success of the NLP population are unknown, but may include lack of suitable habitat, limited reproductive success, poor genetic diversity, disease, or negative environmental impacts. American …

Systematics And Diversification Patterns Of Morphologically And Ecologically Diverse Lineages Of Agaricomycetes: Clavariaceae And Cantharellales, Joshua Mark Birkebak

Doctoral Dissertations

The recent advent of molecular tools and methods to understand the diversity of living organisms allows for exploration of former untestable theories concerning the diversity of fungi. Here we assess the morphologically based classification of the family Clavariaceae in light of molecular phylogenetic reconstruction and propose a revised classification base on natural assemblages. We used stable isotope ratios to uncover a biotrophic nutritional mode for much of the family, which had not been well understood historically. We also investigate several enigmatic lineages of agaricoid or cantharelloid fruiting body producing fungi within a clade of otherwise clavarioid fruiting bodies. We provide …

Linking Physiology And Biogeography: Disentangling The Constraints On The Distributions Of Ant Species, Lacy Danikas Chick

Doctoral Dissertations

Understanding the factors that limit the distribution of species is at the core of ecological and biogeographical research, and is critical if we are to predict the responses of key ecosystem components to ongoing climatic changes. My doctoral research seeks to provide an understanding of how thermal physiology influences species’ distributions and better define the mechanisms underlying geographic variation in biodiversity. By using natural temperature gradients (both elevational and latitudinal) and coupling controlled laboratory experiments with field observations and null modeling approaches, I was able to document the role of inter-specific variation in thermal physiology and, more interesting, inter-population variation …

Molecular Breeding Strategies For Improvement Of Complex Traits In Soybean, Christopher Joseph Smallwood

Doctoral Dissertations

Soybean [Glycine max (L.) Merrill] is the leading oilseed crop grown in the world. Yield, fatty acids, protein, and oil are commercially important soybean traits; thus evaluation of breeding strategies for improvement of these traits is merited. To accomplish this, a comparison of molecular and phenotypic breeding strategies from progeny row selections was performed. From this it was determined that molecular strategies consistently outperformed phenotypic selections (PS) in the progeny row stage for soybean yield, fatty acids, protein, and oil. For yield, Epistacy was the preferred selection method. For fatty acids, protein, and oil, the genomic selection (GS) strategies were …

Multipartite Graph Algorithms For The Analysis Of Heterogeneous Data, Charles Alexander Phillips

Doctoral Dissertations

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of …

Brown And Beige Adipocytes: Effects Of Inflammation And Nutritional Intervention, Jiyoung Bae

Doctoral Dissertations

Recent findings of brown adipocytes and brown-like or beige adipocytes, capable of dissipating energy as heat, in adult humans have promised new hope for obesity treatment and prevention. Understanding of the regulation of brown and beige adipocytes will provide novel strategies to reach the goal. Pattern recognition receptors (PRR) are responsible for inflammation in adipose tissue, which leads to adipose dysfunction and obesity associated chronic diseases. It has been shown that PRR activation induces inflammation, leading to insulin resistance in white adipocytes and white adipose tissue (WAT). However, the roles of PRR activation in brown adipocytes and brown adipose tissue …

Application Of Hidden Markov Model Based Methods For Gaining Insights Into Protein Domain Evolution And Function, Amit Anil Upadhyay

Doctoral Dissertations

With the explosion in the amount of available sequence data, computational methods have become indispensable for studying proteins. Domains are the fundamental structural, functional and evolutionary units that make up proteins. Studying protein domains is an important part of understanding protein function and evolution. Hidden Markov Models (HMM) are one of the most successful methods that have been applied for protein sequence and structure analysis. In this study, HMM based methods were applied to study the evolution of sensory domains in microbial signal transduction systems as well as functional characterization and identification of cellulases in metagenomics datasets. Use of HMM …

Bacterial Diversity And Function Within An Epigenic Cave System And Implications For Other Limestone Cave Systems, Kathleen Merritt Brannen-Donnelly

Doctoral Dissertations

There are approximately 48,000 known cave systems in the United States of America, with caves formed in carbonate karst terrains being the most common. Epigenic systems develop from the downward flow of meteoric water through carbonate bedrock and the solutional enlargement of interconnected subsurface conduits. Despite carbonate karst aquifers being globally extensive and important drinking water sources, microbial diversity and function are poorly understood compared to other Earth environments. After several decades of research, studies have shown that microorganisms in caves affect water quality, rates of carbonate dissolution and precipitation, and ecosystem nutrition through organic matter cycling. However, limited prior …

Applications Of Evolutionary Bioinformatics In Basic And Biomedical Research, Ogun Adebali

Doctoral Dissertations

With the revolutionary progress in sequencing technologies, computational biology emerged as a game-changing field which is applied in understanding molecular events of life for not only complementary but also exploratory purposes. Bioinformatics resources and tools significantly help in data generation, organization and analysis. However, there is still a need for developing new approaches built based on a biologist’s point of view. In protein bioinformatics, there are several fundamental problems such as (i) determining protein function; (ii) identifying protein-protein interactions; (iii) predicting the effect of amino acid variants. Here, I present three chapters addressing these problems from an evolutionary perspective. Firstly, …

Epidemiology Of Select Species Of Filarial Nematodes In Free-Ranging Moose (Alces Alces) Of North America, Caroline Mae Grunenwald

Doctoral Dissertations

North American moose (Alces alces) are a culturally and economically valued species. Recent population declines raise concern for the survivability of this natural resource. The Minnesota population has experienced the most dramatic decline, with a 60% loss in total numbers since 2006. Nematode parasites, particularly some species of filarids, are important pathogens of moose and could be contributing to morbidity and mortality. This study investigates the eco-epidemiology of two filarial parasites of moose: Rumenfilaria andersoni and Elaeophora schneideri. By surveying cervid species from six U.S. states, we discovered R. andersoni was present in moose from all sample locations …

Confirming Resistance To Prodiamine And Glyphosate In A Single Annual Bluegrass (Poa Annua L.) Biotype From Tennessee, Shane Matthew Breeden

Masters Theses

Annual bluegrass (Poa annua L.; POAAN) is a cool-season weed that commonly infests warm-season turfgrasses during winter dormancy. In spring 2012, poor POAAN control (<50%) was reported on golf course roughs in Alcoa, TN (35.75 °N, -83.88 °W) following treatment with a tank mixture of prodiamine (1120 g ha^-1[hectare]) and glyphosate (840 g ae ha^-1) during bermudagrass dormancy. The objective of this research was to determine if this POAAN biotype was resistant to prodiamine and glyphosate.

Using mature plants from the field, 81 of the 100 selections were not controlled by glyphosate and prodiamine; 96 of the 100 selections were not controlled by glyphosate, while 84 were unaffected by prodiamine. Only a single plant sampled was susceptible to both herbicides. …

Impact Of Milk Production Level On Beef Cow-Calf Productivity In Tennessee, Sarah Rebecca Edwards

Masters Theses

The beef cattle industry tends to focus on selecting production traits with the purpose of maximizing cow-calf performance. One such trait is milking ability, which is considered the primary influence on weaning weight of the calf. But, it can also have a negative effect on cow reproductive efficiency and cost of production. Therefore, the objective of this study was to determine the effect of actual milk yield on reproductive performance, circulating blood metabolites, and calf performance in beef cows in Tennessee. Data were collected from 239, 3- to 9-yr-old Angus sired beef cows from 3 research centers across Tennessee. On …

Improving Management And Species Selection Of Warm-Season Forage Grasses For Southeast Production Systems, Christine Helen Gelley

Masters Theses

Beef producers need drought tolerant options when selecting forage grasses and also practical methods to estimate forage nutritive value, which this study aims to provide for warm-season grasses. The objective of the first experiment was to develop estimates of warm-season forage nutritive value and herbage mass based on harvest timing. The experiment was conducted from 2013 to 2015 at the University of Tennessee Plateau AgResearch and Education Center (PREC) in Crossville, TN. Four species were evaluated, each for two years: bermudagrass [Cynodon dactylon (L.) Pers. cv. Vaughn’s # 1], switchgrass [Panicum virgatum (L.) cv. Alamo], sorghum-sudangrass [Sorghum …

Efficacy Of Visual Surveys For White-Nose Syndrome At Bat Hibernacula, Amanda Frances Janicki

Masters Theses

White-Nose Syndrome (WNS) is an epizootic disease in hibernating bats caused by the fungus Pseudogymnoascus destructans. Surveillance for P. destructans at bat hibernacula consists primarily of visual surveys of bats, collection of potentially infected bats, and submission of these bats for laboratory testing. Cryptic infections (bats that are infected but display no visual signs of fungus) could lead to the mischaracterization of the infection status of a site and the inadvertent spread of P. destructans. We determined the efficacy of visual detection of P. destructans by examining visual signs and molecular detection of P. …

Analysis Of Beef Cattle Producers’ Propensity To Adopt Pasture Management And Prescribed Grazing East Of The 100th Meridian, Kristen Elizabeth Oliver

Masters Theses

Pasture management and grazing practices affect animal productivity, soil carbon storage and soil and water quality. Poor pasture and grazing management practices can cause soil erosion, nitrogen leaching, and runoff into streams and waterways. Based on a survey of cattle farmers east of the 100^th meridian, the following two papers estimate how farm operator, farming operation, and attitudinal variables influence the propensity to use pasture management and prescribed grazing, as well as use of specific pasture management and prescribed grazing practices.

Key findings from the first paper are that individual pasture management and prescribed grazing practices are strong indicators …

Removal Of Trace Organic Compounds In Domestic Wastewater Using Recirculating Packed-Bed Media Filters, Brittani Nikole Perez

Masters Theses

Pharmaceuticals and personal care products (PPCPs) are commonly detected in the environment resulting from their survival from conventional wastewater treatment systems. More information is needed about the fate and transfer of these trace organic compounds in domestic wastewater and their associated risks so that efficient strategies for their removal can be developed for both large/small scale treatment systems. This study aimed to determine whether onsite wastewater treatment systems were capable of providing PPCP removal, in addition to quantifying different forms of removal (biodegradation/sorption). A column study was constructed to determine the removal efficiencies of 3 target PPCPs, endocrine disrupting compound …

Evaluation Of A Natural Antimicrobial-Based Sanitizer As An Alternative To Chlorine For Reducing Foodborne Pathogenic Bacteria On Organic Produce, Ellen Rebecca Simmons

Masters Theses

There is a need for the development of a “natural” sanitizing agent to reduce or eliminate foodborne pathogens that meets USDA organic standards, as an alternative to chlorine. The sanitizer needs to eliminate foodborne pathogens and prevent cross contamination in rinse liquids in the presence of organic matter. In this study, the focus was to evaluate a natural antimicrobial-based sanitizing (NABS) agent in rinse liquids to determine if it was capable of eliminating foodborne pathogens on organic produce through cross-contamination studies. Five-serovar/strain cocktails of pathogenic bacteria were combined to form an inoculum cocktail, which was used to inoculate the produce. …

Potential Interaction Between Pre- And Post-Emergence Herbicides And The Efficacy Of Insecticide And Fungicide Seed Treatments In Cotton, Cory Joseph Vineyard

Masters Theses

An apparent reduction in the performance of neonicotinoid seed treatments in controlling thrips, especially in cotton, has been observed, which has coincided with the increased use of both pre- and post-emergence herbicides to control glyphosate-resistant weeds. The objective of this research was to evaluate the potential interactions of both pre- and post-emergence herbicides on the efficacy of insecticide and fungicide seed treatments in cotton

Aldicarb along with imidacloprid and thiamethoxam seed treatments reduced thrips numbers compared with non-treated seed. However, thiamethoxam did not provide effective control. Some pre-emergence herbicide treatments reduced plant health. While there was evidence that thrips injury …

A New Adaptive Landscape: Urbanization As A Strong Evolutionary Force, Lauren Christie Breza

Masters Theses

Urbanization is rapidly increasing as human population growth steadily grows, but there is little consensus of the ecological consequence of this population shift and almost no information of the evolutionary consequences for local biodiversity. Nearly two-thirds of the world’s population will live in city centers by 2050 with profound impacts on landscapes that can act as important agents of selection. This study aims to identify 1) the net effect of urbanization on species richness, 2) how phylogenetic diversity varies between urban and rural sites, and 3) the strength of urbanization as a selection pressure. First, a meta-analysis was conducted in …

Subfunctionalization Of Ethylene Receptors And Homology Modeling Of Cytosolic Domains In Arabidopsis Thaliana, Sai Keerthana Wuppalapati

Masters Theses

Ethylene is a gaseous phytohormone that initiates and modulates several mechanisms related to growth and development in plants through a family of five disulphide-linked receptor dimers. Although the ethylene receptors are very similar in their structures, they have diverse functions with both overlapping and non-overlapping roles. Silver ions are able to support ethylene binding to the receptors but it is also interesting to note that ethylene responses are blocked in the presence of silver. A part of the present study identified that ETR1 receiver domain has little or no role in mediating responses to silver ions, supported by data obtained …

Evaluation Of Reproductive Efficiency In Lactating Dairy Cows Through Physiologic Evaluation And Synchronization Modification, Charles Dexter Young

Doctoral Dissertations

Reproductive performance of lactating dairy cows has decreased as milk production has increased as a result of genetic selection. Milk production alone is not the reason for decreased reproductive performance, as fertility issues are multifactorial and collaborative. Research chapters contained within have taken an applied approach focusing in two different areas of fertility. One approach was development of an evaluation system to identify lactating cows with decreased fertility prior to breeding; while another approach was to modify an ovulation synchronization protocol during periods of heat stress in order to improve fertility. The first focus was development and evaluation of a …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

Effects Of Low-Dose Naltrexone On Feed Intake, Growth, Endocrine And Immune Parameters In The Recently-Weaned Pig, Ashley Christine Carter

Masters Theses

Weaning is a stressful event for pigs and causes decreased feed intake, poor growth, and increased susceptibility to disease. Previous studies have shown that syndyphalin-33, a synthetic opioid, was effective in increasing feed intake, abrogating the changes in appetite regulating genes during weaning, and abrogating the effects of a salmonella challenge on immune cells in newly-weaned pigs. However, there are several concerns associated with the administration of an opioid in commercial swine operations. Low-dose naltrexone (an opioid antagonist) has been used to alleviate symptoms from fibromyalgia and Crohn’s disease in humans. As inflammation is a common factor in both auto-immune …

Interactions Among Insect Defoliation, Insecticide Treatments, And Growth Rate In American And Hybrid Chestnuts, Ashley Elizabeth Case

Masters Theses

The American chestnut, Castanea dentata, was once one of the most useful and abundant canopy trees in eastern North American forests. Over the last 200 years, the species has been decimated by two exotic pathogens, Phytophthora cinnamomi and Cryphonectria parasitica, killing millions of trees and reducing surviving Castanea dentata to short-lived sprouts. Cryphonectria parasitica-resistance breeding programs are currently producing advanced backcross generations, which are being compared with pure American chestnut in field tests of growth performance and Cryphonectria parasitica resistance. The Asiatic oak weevil, Cyrtepistomus castaneus, has been identified as a common defoliator of chestnut seedlings in these …

4-H Wildlife Habitat Education Program: A Qualitative Study On Career Exploration, Ronnie Lee Cowan

Masters Theses

There are documented studies on the Wildlife Habitat Education Program (WHEP) that relate to building life skills of participants. However, no literature was found that measured the perceptions of the participants towards a career in wildlife after participating in WHEP. To add validity to the program a focus group was conducted at the Tennessee 4-H wildlife judging contest to describe the WHEP participants’ perceptions of careers in wildlife after the completion of the annual program. Focus group participants indicated that participating in WHEP peaked their interest in wildlife and provided an opportunity to experience the importance of natural resource management.

Effects Of Bedding With Recycled Sand On Lying Behaviors, Udder Hygiene, And Preferences Of Lactating Holstein Dairy Cows, Heather Deanna Ingle

Masters Theses

Effects of bedding with recycled sand and season on lying behaviors, stress, hygiene, and preferences of late-lactation Holstein cows were studied. Cows (n=64) were divided into 4 groups (n=8 per group) per season. In summer (Aug-Sept), cows were balanced by days in milk (268.1±11.9 d) and parity (2.0±0.2). In winter (Jan-Feb), mean DIM was 265.5±34.1 d. Cows were assigned to one of two treatments (trt) using a crossover design with each trt lasting 7-d (no-choice phase): bedding with recycled sand (RS; n=32) or control (CO; clean sand; n=32). Stocking density was maintained at 100%. Choice phase allowed a cow to …