DEVELOPMENT AND APPLICATIONS OF GENOMIC RESOURCES FOR TWO NORTH AMERICAN HARDWOOD TAXA

Hardwoods comprise about half of the biomass of forestlands in North America and present many uses including economic, ecological and aesthetic functions. Forest trees rely on the genetic variation within tree populations to overcome the many biotic, abiotic, anthropogenic factors which are further worsened by climate change, that threaten their continued survival and functionality. To harness these inherent genetic variations of tree populations, informed knowledge of the genomic resources and techniques, which are currently lacking or very limited, are imperative for forest managers. The current study therefore aimed to develop genomic microsatellite markers for the leguminous tree species, honey locust, Gleditsia triacanthos L. and test their applicability in assessing genetic variation, estimation of gene flow patterns and identification of a full-sib mapping population. We also aimed to test the usefulness of already developed nuclear and gene-based microsatellite markers in delineation of species and taxonomic relationships between four of the taxonomically difficult Section Lobatae species (Quercus coccinea, Q. ellipsoidalis, Q. rubra and Q. velutina. We recorded 100% amplification of G. triacanthos genomic microsatellites developed using Illumina sequencing techniques in a panel of seven unrelated individuals with 14 of these showing high polymorphism and reproducibility. When characterized in 36 natural population samples, we recorded 20 alleles per locus with no indication for null alleles at 13 of the 14 microsatellites. This is the first report of genomic microsatellites for this species. Honey locust trees occur in fragmented populations of abandoned farmlands and pastures and is described as essentially dioecious. Pollen dispersal if the main source of gene flow within and between populations with the ability to offset the effects of random genetic drift. Factors known to influence gene include fragmentation and degree of isolation, which make the patterns gene flow in fragmented populations of honey locust a necessity for their sustainable management. In this follow-up study, we used a subset of nine of the 14 developed gSSRs to estimate gene flow and identify a full-sib mapping population in two isolated fragments of honey locust. Our analyses indicated that the majority of the seedlings (65-100% - at both strict and relaxed assignment thresholds) were sired by pollen from outside the two fragment populations. Only one selfing event was recorded confirming the functional dioeciousness of honey locust and that the seed parents are almost completely outcrossed. From the Butternut Valley, TN population, pollen donor genotypes were reconstructed and used in paternity assignment analyses to identify a relatively large full-sib family comprised of 149 individuals, proving the usefulness of isolated forest fragments in identification of full-sib families. In the Ames Plantation stand, contemporary pollen dispersal followed a fat-tailed exponential-power distribution, an indication of effective gene flow. Our estimate of δ was 4,282.28 m, suggesting that insect pollinators of honey locust disperse pollen over very long distances. The high proportion of pollen influx into our sampled population implies that our fragment population forms part of a large effectively reproducing population. The high tendency of oak species to hybridize while still maintaining their species identity make it difficult to resolve their taxonomic relationships. Oaks of the section Lobatae are famous in this regard and remain unresolved at both morphological and genetic markers. We applied 28 microsatellite markers including outlier loci with potential roles in reproductive isolation and adaptive divergence between species to natural populations of four known interfertile red oaks, Q. coccinea, Q. ellpsoidalis, Q. rubra and Q. velutina. To better resolve the taxonomic relationships in this difficult clade, we assigned individual samples to species, identified hybrids and introgressive forms and reconstructed phylogenetic relationships among the four species after exclusion of genetically intermediate individuals. Genetic assignment analyses identified four distinct species clusters, with Q. rubra most differentiated from the three other species, but also with a comparatively large number of misclassified individuals (7.14%), hybrids (7.14%) and introgressive forms (18.83%) between Q. ellipsoidalis and Q. velutina. After the exclusion of genetically intermediate individuals, Q. ellipsoidalis grouped as sister species to the largely parapatric Q. coccinea with high bootstrap support (91 %). Genetically intermediate forms in a mixed species stand were located proximate to both potential parental species, which supports recent hybridization of Q. velutina with both Q. ellipsoidalis and Q. rubra. Analyses of genome-wide patterns of interspecific differentiation can provide a better understanding of speciation processes and taxonomic relationships in this taxonomically difficult group of red oak species.

DESIGN, SYNTHESIS AND APPLICATIONS OF FLUORESCENT AND ELECTROCHEMICAL PROBES

“Seeing is believing” the proverb well suits for fluorescent imaging probes. Since we can selectively and sensitively visualize small biomolecules, organelles such as lysosomes, neutral molecules, metal ions, anions through cellular imaging, fluorescent probes can help shed light on the physiological and pathophysiological path ways. Since these biomolecules are produced in low concentrations in the biochemical pathways, general analytical techniques either fail to detect or are not sensitive enough to differentiate the relative concentrations. During my Ph.D. study, I exploited synthetic organic techniques to design and synthesize fluorescent probes with desirable properties such as high water solubility, high sensitivity and with varying fluorescent quantum yields. I synthesized a highly water soluble BOIDPY-based turn-on fluorescent probe for endogenous nitric oxide. I also synthesized a series of cell membrane permeable near infrared (NIR) pH activatable fluorescent probes for lysosomal pH sensing. Fluorescent dyes are molecular tools for designing fluorescent bio imaging probes. This prompted me to design and synthesize a hybrid fluorescent dye with a functionalizable chlorine atom and tested the chlorine re-activity for fluorescent probe design. Carbohydrate and protein interactions are key for many biological processes, such as viral and bacterial infections, cell recognition and adhesion, and immune response. Among several analytical techniques aimed to study these interactions, electrochemical bio sensing is more efficient due to its low cost, ease of operation, and possibility for miniaturization. During my Ph.D., I synthesized mannose bearing aniline molecule which is successfully tested as electrochemical bio sensor. A Ferrocene-mannose conjugate with an anchoring group is synthesized, which can be used as a potential electrochemical biosensor.

IDENTIFICATION OF GENES CONTROLLING BIOLOGICAL PROCESSES AND PATHWAYS THROUGH STATISTICAL ANALYSIS AND NETWORK RECONSTRUCTION

The developmental processes and functions of an organism are controlled by the genes and the proteins that are derived from these genes. The identification of key genes and the reconstruction of gene networks can provide a model to help us understand the regulatory mechanisms for the initiation and progression of biological processes or functional abnormalities (e.g. diseases) in living organisms. In this dissertation, I have developed statistical methods to identify the genes and transcription factors (TFs) involved in biological processes, constructed their regulatory networks, and also evaluated some existing association methods to find robust methods for coexpression analyses. Two kinds of data sets were used for this work: genotype data and gene expression microarray data. On the basis of these data sets, this dissertation has two major parts, together forming six chapters. The first part deals with developing association methods for rare variants using genotype data (chapter 4 and 5). The second part deals with developing and/or evaluating statistical methods to identify genes and TFs involved in biological processes, and construction of their regulatory networks using gene expression data (chapter 2, 3, and 6). For the first part, I have developed two methods to find the groupwise association of rare variants with given diseases or traits. The first method is based on kernel machine learning and can be applied to both quantitative as well as qualitative traits. Simulation results showed that the proposed method has improved power over the existing weighted sum method (WS) in most settings. The second method uses multiple phenotypes to select a few top significant genes. It then finds the association of each gene with each phenotype while controlling the population stratification by adjusting the data for ancestry using principal components. This method was applied to GAW 17 data and was able to find several disease risk genes. For the second part, I have worked on three problems. First problem involved evaluation of eight gene association methods. A very comprehensive comparison of these methods with further analysis clearly demonstrates the distinct and common performance of these eight gene association methods. For the second problem, an algorithm named the bottom-up graphical Gaussian model was developed to identify the TFs that regulate pathway genes and reconstruct their hierarchical regulatory networks. This algorithm has produced very significant results and it is the first report to produce such hierarchical networks for these pathways. The third problem dealt with developing another algorithm called the top-down graphical Gaussian model that identifies the network governed by a specific TF. The network produced by the algorithm is proven to be of very high accuracy.

Volcanic processes and human exposure as elements to build a risk model for Volcan de Fuego, Guatemala

The activity of Fuego volcano during the 1999 - 2013 eruptive episode is studied through field, remote sensing and observatory records. Mapping of the deposits allows quantifying the erupted volumes and areas affected by the largest eruptions during this period. A wide range of volcanic processes results in a diversity of products and associated deposits, including minor airfall tephra, rockfall avalanches, lava flows, and pyroclastic flows. The activity can be characterized by long term, low level background activity, and sporadic larger explosive eruptions. Although the background activity erupts lava and ash at a low rate (~ 0.1 m3/s), the persistence of such activity over time results in a significant contribution (~ 30%) to the eruption budget during the studied period. Larger eruptions produced the majority of the volume of products during the studied period, mainly during three large events (May 21, 1999, June 29, 2003, and September 13, 2012), mostly in the form of pyroclastic flows. A total volume of ~ 1.4 x 108 m3 was estimated from the mapped deposits and the estimated background eruption rate. Posterior remobilization of pyroclastic flow material by stream erosion in the highly confined Barranca channels leads to lahar generation, either by normal rainfall, or by extreme rainfall events. A reassessment of the types of products and volumes erupted during the decade of 1970's allows comparing the activity happening since 1999 with the older activity, and suggests that many of the eruptive phenomena at Fuego may have similar mechanisms, despite the differences in scale between. The deposits of large pyroclastic flows erupted during the 1970's are remarkably similar in appearance to the deposit of pyroclastic flows from the 1999 - 2013 period, despite their much larger volume; this is also the case for prehistoric eruptions. Radiocarbon dating of pyroclastic flow deposits suggests that Fuego has produced large eruptions many times during the last ~ 2 ka, including larger eruptions during the last 500 years, which has important hazard implications. A survey was conducted among the local residents living near to the volcano, about their expectations of possible future crises. The results show that people are aware of the risk they could face in case of a large eruption, and therefore they are willing to evacuate in such case. However, their decision to evacuate may also be influenced by the conditions in which the evacuation could take place. If the evacuation represents a potential loss of their livelihood or property they will be more hesitant to leave their villages during a large eruption. The prospect of facing hardship conditions during the evacuation and in the shelters may further cause reluctance to evacuate. A short discussion on some of the issues regarding risk assessment and management through an early warning system is presented in the last chapter.

SECURITY, PRIVACY AND APPLICATIONS IN VEHICULAR AD HOC NETWORKS

With wireless vehicular communications, Vehicular Ad Hoc Networks (VANETs) enable numerous applications to enhance traffic safety, traffic efficiency, and driving experience. However, VANETs also impose severe security and privacy challenges which need to be thoroughly investigated. In this dissertation, we enhance the security, privacy, and applications of VANETs, by 1) designing application-driven security and privacy solutions for VANETs, and 2) designing appealing VANET applications with proper security and privacy assurance. First, the security and privacy challenges of VANETs with most application significance are identified and thoroughly investigated. With both theoretical novelty and realistic considerations, these security and privacy schemes are especially appealing to VANETs. Specifically, multi-hop communications in VANETs suffer from packet dropping, packet tampering, and communication failures which have not been satisfyingly tackled in literature. Thus, a lightweight reliable and faithful data packet relaying framework (LEAPER) is proposed to ensure reliable and trustworthy multi-hop communications by enhancing the cooperation of neighboring nodes. Message verification, including both content and signature verification, generally is computation-extensive and incurs severe scalability issues to each node. The resource-aware message verification (RAMV) scheme is proposed to ensure resource-aware, secure, and application-friendly message verification in VANETs. On the other hand, to make VANETs acceptable to the privacy-sensitive users, the identity and location privacy of each node should be properly protected. To this end, a joint privacy and reputation assurance (JPRA) scheme is proposed to synergistically support privacy protection and reputation management by reconciling their inherent conflicting requirements. Besides, the privacy implications of short-time certificates are thoroughly investigated in a short-time certificates-based privacy protection (STCP2) scheme, to make privacy protection in VANETs feasible with short-time certificates. Secondly, three novel solutions, namely VANET-based ambient ad dissemination (VAAD), general-purpose automatic survey (GPAS), and VehicleView, are proposed to support the appealing value-added applications based on VANETs. These solutions all follow practical application models, and an incentive-centered architecture is proposed for each solution to balance the conflicting requirements of the involved entities. Besides, the critical security and privacy challenges of these applications are investigated and addressed with novel solutions. Thus, with proper security and privacy assurance, these solutions show great application significance and economic potentials to VANETs. Thus, by enhancing the security, privacy, and applications of VANETs, this dissertation fills the gap between the existing theoretic research and the realistic implementation of VANETs, facilitating the realistic deployment of VANETs.

Beech bark disease distribution and resistance in Michigan and fungal endophyte ecology of resistant and susceptible beech (Fagus grandifolia Ehrh.)

Beech bark disease (BBD), a non-native association of the fungal pathogen Neonectria faginata and the beech scale insect Cryptococcus fagisuga, has dramatically affected American beech within North American forests. To monitor the spread and effects of BBD in Michigan, a network of forest health monitoring plots was established in 2001 following the disease discovery in Ludington State Park (Mason County). Forest health canopy condition and basic forestry measurements including basal area were reassessed on beech trees in these plots in 2011 and 2012. The influence of bark-inhabiting fungal endophytes on BBD resistance was investigated by collecting cambium tissue from apparently resistant and susceptible beech. Vigor rating showed significant influences of BBD in sample beech resulting in reduced health and substantiated by significant increases of dead beech basal area over time. C. fagisuga distribution was found to be spatially clustered and widespread in the 22 counties in Michigan's Lower Peninsula which contained monitoring plots. Neonectria has been found in Emmet, Cheboygan and Wexford in the Lower Peninsula which may coincide with additional BBD introduction locations. Surveys for BBD resistance resulted in five apparently resistant beech which were added to a BBD resistance database. The most frequently isolated endophytes from cambium tissue were identified by DNA sequencing primarily as Deuteromycetes and Ascomycetes including Chaetomium globosum, Neohendersonia kickxii and Fusarium flocciferum. N. faginata in antagonism trials showed significant growth reduction when paired with three beech fungal endophytes. The results of the antagonism trial and decay tests indicate that N. faginata may be a relatively poor competitor in vivo with limited ability to degrade cellulose.

Spatial and temporal patterns in ungulate-ecosystem interactions

Ungulates are important components of a variety of ecosystems worldwide. This dissertation integrates aspects of ungulate and forest ecology to increase our understanding of how they work together in ways that are of interest to natural resource managers, educators, and those who are simply curious about nature. Although animal ecology and ecosystem ecology are often studied separately, one of the general goals of this dissertation is to examine how they interact across spatial and temporal scales. Forest ecosystems are heterogeneous across a range of scales. Spatial and temporal habitat use patterns of forest ungulates tend to be congregated in patches where food and/or cover are readily available. Ungulates interact with ecosystem processes by selectively foraging on plants and excreting waste products in concentrated patches. Positive feedbacks may develop where these activities increase the value of habitat through soil fertilization or the alteration of plant chemistry and architecture. Heterogeneity in ecosystem processes and plant community structure, observed at both stand and local scales, may be the integrated outcome of feedbacks between ungulate behavior and abiotic resource gradients. The first chapter of this dissertation briefly discusses pertinent background information on ungulate ecology, with a focus on white-tailed deer (Odocoileus virginianus) in the Upper Great Lakes region and moose (Alces acles) in Isle Royale National Park, Michigan, USA. The second chapter demonstrates why ecological context is important for studying ungulate ecology in forest ecosystems. Excluding deer from eastern hemlock (Tsuga canadensis) stands, which deer use primarily as winter cover, resulted in less spatial complexity in soil reactive nitrogen and greater complexity in diffuse light compared to unfenced stands. The spatial patterning of herbaceous-layer cover was more similar to nitrogen where deer were present, and was a combination of nitrogen and light within deer exclosures. This relationship depends on the seasonal timing of deer habitat use because deer fertilize the soil during winter, but leave during the growing season. The third chapter draws upon an eight-year, 39-stand data set of deer fecal pellet counts in hemlock stands to estimate the amount of nitrogen that deer are depositing in hemlock stands each winter. In stands of high winter deer use, deer-excreted nitrogen inputs consistently exceeded those of atmospheric deposition at the stand scale. At the neighborhood scale, deer-excreted nitrogen was often in excess of atmospheric deposition due to the patchy distribution of deer habitat use. Spatial patterns in habitat use were consistent over the eight-year study at both stand and neighborhood scales. The fourth chapter explores how foraging selectivity by moose interacts with an abiotic resource gradient to influence forest structure and composition. Soil depth on Isle Royale varies from east to west according to glacial history. Fir saplings growing in deeper soils on the west side are generally more palatable forage for moose (lower foliar C:N) than those growing in shallower soils on the east side. Therefore, saplings growing in better conditions are less likely to reach the canopy due to moose browsing, and fir is a smaller overstory component on the west side. Lastly, chapter five focuses on issues surrounding eastern hemlock regeneration failure, which is a habitat type that is important to many wildlife species. Increasing hemlock on the landscape is complicated by several factors including disturbance regime and climate change, in addition to the influence of deer.