Modeling Hydrological Processes and Key Factors Influencing Nonpoint Source Pollution in Agricultural and Urban Settings

Nonpoint-source pollution from agricultural and urban landscape is a major threat to water quality worldwide. This doctoral research aims to assess the spatiotemporal variations of nonpoint-source pollution and elucidate key factors at play in representative agricultural and urban settings in the US Pacific Northwest (PNW). The main objectives were to:1) elucidate the long-term historical soil erosion trend, as affected by climatic and management conditions;2) assess changes in water erosion as impacted by the projected future climate and the effect of conservation practices using WEPP; and3) optimize placement of rain gardens in an urbanizing watershed, south Puget Sound, using the Hydrologic Sensitivity Index (HSI) method.For the first study, I delineated a watershed within the low-, intermediate-, and high-precipitation zones of eastern Washington, and simulated water erosion over two time periods: past and present, under different tillage practices and crop rotations. The average annual erosion rates decreased from the past by 32%, 57%, and 70%, respectively, for the three watersheds. The decrease was due to the combined effects of changing climate and implementation of conservation practices.For the second study, I modeled water erosion for the same three watersheds for two time periods: historical and future using downscaled climates. Future average annual precipitation and daily temperature increase by 4–6% and 7–10%, respectively. Projected annual water erosion generally decreased by 0–4% for the three watersheds, owing to improvement in winter conditions. Future annual water erosion exceeds 50 Mg ha−1 in areas with steeper slopes and years with wheat, especially in intermediate-, and high-precipitation zones. I recommend targeted land management practices for erosion reduction.In the third study, I used the HSI approach to identify areas prone to runoff generation and suitable areas for rain gardens, a small-scale Green Stormwater Infrastructure (GSI). I conducted hydrologic modeling to assess the adequacy of the HSI method. The simulated runoff was positively correlated with HSI. The locations most suitable for rain gardens were concentrated in the northeastern-central parts of the study watershed. This study demonstrated the adequacy of HSI method and provided a strategy for practitioners and regulatory personnel in optimizing the placement of rain gardens.Findings from this dissertation advance the understanding of nonpoint-source pollution and contribute to conservation planning in both agricultural and urban areas

Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype

The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the heterogeneity in GC content is being reinforced in the avian genome. Despite this discrepancy, which remains unexplained, examinations of individual substitution frequencies in mammals and birds are both consistent with the gBGC model of isochore evolution. On the other hand, a negative correlation between substitution and recombination rate found in the chicken genome is inconsistent with the gBGC model. It should therefore be important to consider along with gBGC other consequences of recombination on the origin and fate of mutations, as well as to account for relationships between recombination rate and other genomic features. We therefore developed an analytical model to describe the substitution patterns found in the chicken genome, and further investigated the relationships between substitution patterns and several genomic features in a rigorous statistical framework. Our analysis indicates that GC content itself, either directly or indirectly via interrelations to other genomic features, has an impact on the substitution pattern. Further, we suggest that this phenomenon is particularly visible in avian genomes due to their unusually low rate of chromosomal evolution. Because of this, interrelations between GC content and other genomic features are being reinforced, and are as such more pronounced in avian genomes as compared with other vertebrate genomes with a less stable karyotype

Identifying Priority Sites for Rain Gardens in Lower Puyallup River Watershed

Stormwater runoff is a primary carrier of pollutants to the nearby streams and lakes. Green stormwater infrastructure (GSI) is built to intercept stormwater runoff to mitigate peak flows and stormwater pollutants before reaching surface waters. A rain garden is a type of GSI comprising a plant-soil system where water retention is maximized through infiltration and storage. Proper placement of rain gardens within the watershed is crucial to maximizing their cost-effectiveness. The Lower Puyallup River Watershed, situated in South Puget Sound, consists of primarily residential areas of the cities of Puyallup and Tacoma. Preservation of water quality is essential as the streams and rivers in the watershed are critical aquatic habitats for Chinook and Coho salmon return for spawning. The study\u27s objective is to develop a framework to identify suitable sites for rain gardens in an urbanizing watershed. An indexing approach to identify Hydrological Sensitive Areas (HSA) was adopted, in which we consider the topography, runoff contributing area, soil depth, and hydraulic conductivity. The Topographic Wetness Index (TWI) and Soil Water Storage Capacity (SWSC) were computed to obtain the Hydrologic Sensitivity Index (HSI). Areas considered infeasible per criteria specified by state and county regulations were removed, and HSI was classified based on suitability for the construction of rain gardens. This study provides a practical, scalable, and portable tool for prioritizing the placement of GSI for stormwater runoff management

A Wright-Fisher graph model and the impact of directional selection on genetic variation

We introduce a multi-allele Wright-Fisher model with non-recurrent, reversible mutation and directional selection. In this setting, the allele frequencies at a single locus track the path of a hybrid jump-diffusion process with state space given by the vertex and edge set of a graph. Vertices represent monomorphic population states and edge-positions mark the biallelic proportions of ancestral and derived alleles during polymorphic segments. We derive the stationary distribution in mutation-selection-drift equilibrium and obtain the expected allele frequency spectrum under large population size scaling. For the extended model with multiple independent loci we derive rigorous upper bounds for a wide class of associated measures of genetic variation. Within this framework we present mathematically precise arguments to conclude that the presence of directional selection reduces the magnitude of genetic variation, as constrained by the bounds for neutral evolution

Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Local variation in neutral substitution rate across mammalian genomes is governed by several factors, including sequence context variables and structural variables. In addition, the interplay of replication and transcription, known to induce a strand bias in mutation rate, gives rise to variation in substitutional strand asymmetries. Here, we address the conservation of variation in mutation rate and substitutional strand asymmetries using primate- and rodent-specific repeat elements located within the introns of protein-coding genes. We find significant but weak conservation of local mutation rates between human and mouse orthologs. Likewise, substitutional strand asymmetries are conserved between human and mouse, where substitution rate asymmetries show a higher degree of conservation than mutation rate. Moreover, we provide evidence that replication and transcription are correlated to the strength of substitutional asymmetries. The effect of transcription is particularly visible for genes with highly conserved gene expression. In comparison with replication and transcription, mutation rate influences the strength of substitutional asymmetries only marginally

Tunkeutumisenesto ja havainnointi käytönvalvontajärjestelmissä

Tässä insinöörityössä tutkittiin tunkeutumisenesto- ja havainnointijärjestelmien soveltuvuutta nykyaikaisiin käytönvalvontajärjestelmiin. Työ tehtiin Helsingin Energialle, joka on merkittävä energiapalveluita tarjoava yritys Suomessa. Työssä perehdyttiin ensin teoreettisella tasolla käytönvalvontajärjestelmien arkkitehtuuriin, komponentteihin ja tietoturvavaatimuksiin. Lisäksi tutustuttiin yleisimpiin käytössä oleviin käytönvalvontaprotokolliin ja niiden rakenteisiin. Tämän jälkeen työssä selvitettiin tunkeutumisenesto- ja havainnointitekniikoiden toimintaa sekä suunnittelun perusteita. Tämä insinöörityö tuotti myös käytönvalvontajärjestelmiin suunnitellun tunkeutumisenesto- ja havainnointijärjestelmän vaatimusmäärittelyn ja toteutussuunnitelman. Työn tuloksena todettiin tunkeutumisenesto- ja havainnointijärjestelmien protokollakuvauksien tarjonnan olevan niukkaa Pohjoismaissa käytetyille käytönvalvontaprotokollille. Lisäksi kuvausten käyttöönottoon tulee suhtautua varauksella järjestelmien kriittisyyden vuoksi. IDPS-järjestelmien todettiin kuitenkin nostavan käytönvalvontajärjestelmien tieto-turvatasoa muilla ominaisuuksillaan. Työssä painotettiin lisäksi tunkeutumisenesto- ja havainnointijärjestelmän integroinnin tärkeyttä ylläpito- ja hallintaprosesseihin, sekä elinkaaresta huolehtimista.The purpose of this study was to research possibilities for implementing intrusion prevention and detection systems into modern SCADA networks. This study was carried out for Helsinki Energy, a significant energy service provider in Finland. The first part discusses the architecture of SCADA networks, its components and data security requirements on a theoretical level, as well as the most common SCADA protocols and structures. The second part studies the function of intrusion prevention and detection and the basis for its design. This study also defined the requirements as well as laid out an implementation plan for intrusion prevention and detection in SCADA networks. The results of this study show that the supply of intrusion prevention and detection protocol filters is insufficient for SCADA networks used in the Nordic countries. Furthermore, the implementation of protocol filters must be viewed critically. Nevertheless, the IDPS systems still seem to raise the data security level of SCADA networks. It was concluded that the integration of intrusion prevention and detection into maintenance and management practice is as important as the lifecycle. This study was successful in defining the requirements as well as in creating an implementation plan for intrusion prevention and detection in SCADA networks

Molecular evolution of genes in avian genomes

Nam K, Mugal C, Nabholz B, et al. Molecular evolution of genes in avian genomes. Genome Biology. 2010;11(6): R68.Background: Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species. Results: We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an overrepresentation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton. Conclusions: Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable