As the field of genomics continues to grow, there is an overwhelming need for robust ways to assemble entire genomes, yet there is little guidance on what software best achieves this goal. An assessment of available genome assemblers is needed to improve assembly procedures. Genome assemblers output draft assemblies consisting of DNA scaffolds that are permeated with errors inherent to sequencing data, like wrong number of repeats, misjoins, inversions, missing sequencing, and extraneous sequences. These draft assemblies can then be input into an experimental assay called HiC that attempts to fix and orient the assemblies by taking into account chromatin contact interactions to elucidate genome architecture. The resulting genome is then more accurate and useful for research purposes. However, given the plethora of genome assembly and HiC software available, navigating each available software is time consuming and often requires extensive testing before actual use can begin. To improve this process, we aim to review several HiC scaffolding software tools for performance and quality, and fine tune their parameters for optimized outcome. This will allow us to suggest which software work best for a range of genomic data as well as provide summary statistics and accuracy measurements for each genome assembler tested. We tested several genome assemblers, including GRAAL and SALSA, which utilize HiC libraries to scaffold draft assemblies. After being produced and corrected through assemblers, these assembled genomes can then be used to advance research in functional genomics, genetic epidemiology, and many other fields reliant on genomic data. It is our goal to improve genome assembly procedures so that more researchers can use open source software to build and understand entire genomes and further the field of genomics.

River ecosystems depend on services salmon populations provide. Coho salmon, Oncorhyncus kisutch, supply valuable nutrients for mammals and birds and offer economic benefits for the Pacific Northwest. Salmon rely on water quality in freshwater streams during successful seasonal spawning. However, for over the past 15 years, research determined that urban stormwater results in the mortality of Coho salmon. Exposure to urban stormwater is toxic to Coho salmon, killing them in hours. This phenomenon is known as pre-spawn mortality (PSM), and it kills salmon before they reproduce. If this phenomenon continues, Coho salmon could go extinct. Previous studies have linked highway runoff and pre-spawn mortality. However, they indicate that basic water quality parameters such as temperature and pH and “typical” stormwater toxicants such as metals and pesticides are not the cause of PSM. Current hypotheses point to an unknown organic contaminant that is linked to urbanization and is probably present from roadways or cars. Previous studies have also shown that bioinfiltration of stormwater through a mixture of sand and compost can protect Coho salmon. The goal of this study was to investigate removal of organic contaminants in a pilot-scale compost-amended bioswale (CABS). The pilot-scale CABS was based on a field-scale bioswale that is operated by WA DOT and located on SR-518. In this study, we developed methods to extract water with suspended sediment (whole water), as well as extract filtered water and total suspended sediment (TSS) separately. Whole water and filtered water were extracted by solid phase extraction (SPE), using Infinity® SPE cartridges. TSS was measured using EPA Method 160.2, and captured solids were extracted with methanol. Extracts were then analyzed by liquid chromatography-high resolution mass spectrometry. These methods were then applied to evaluate removal of organic contaminants in the bioswale, including performance at multiple hydraulic retention times.

Just as mountain-building from the convergence of tectonic plates changes weather patterns, the opposite, monsoons in southwest Asia, may have also influenced the erosion of the Himalayas. Turbidite sediments collected in International Ocean Discovery Program cores from the Bay of Bengal contain material eroded from the Himalaya, which may have been shaken up during monsoon destruction then resettled. Magnetic particles extracted from those turbidites were tested for magnetic properties and identified using scanning electron microscopy. Magnetic minerals positively identified include magnetite and sulfides. Linking these minerals to their sources in rocks and soils from the Indian Subcontinent and the Tibetan Plateau, we will be better able to model the erosion patterns back from 14,000 years ago, potentially correlating heavy storm activity in one region to massive sediment deposition downstream. This data may suggest whether the erosion from weather over a long period of time creates a negative feedback loop causing more intense climates overall. Further data that refines the ages of sediment layers can also relate how the severity of storms affects the increase in mountain erosion and runoff.

Soil contamination occurs when human-made chemicals seep into the ground. It can have negative effects on human and animal health, pollute groundwater, and reduce crop yields. Chlorinated ethenes are toxic chemicals used in degreasing and dry cleaning, and their improper disposal can result in contamination. Before remediation to remove the contaminant happens, the affected site must be assessed. Magnetic susceptibility is a measurement of a substance’s ability to be magnetized when put in a magnetic field. Magnetite, a common mineral with the formula Fe₃O₄, is strongly magnetic and has a high average susceptibility. Indeed, magnetite can dominate the magnetic properties of Earth materials such that magnetic susceptibility can be used as a proxy for magnetite abundance. Soil contaminated with chlorinated ethenes has several biotic and abiotic degradation pathways. One abiotic pathway is through magnetite, which is known to affect the detoxification of this pollutant. Choosing the best pathway is aided by the software tool BioPIC. In this study, soil was analyzed using a protocol developed for frequency-dependent discrete specimen magnetic susceptibility measurements to determine magnetite content, and thus to estimate ethene degradation rates. Frequency-dependent measurements allow for estimating magnetite particle size, which influences reactivity. We also explore other magnetic properties to more conclusively determine magnetite concentration. A further avenue for research in the future would be to discern the source of magnetite in the soil, whether it is transported by water or air, precipitated from chemical solutions, or synthesized by certain bacteria. Abiotic degradation of ethenes is just one parameter to consider in an overall remediation strategy. Options for remediation include removing and disposing of the affected soil, containing the soil in place, aerating the soil, and using microorganisms to digest the pollutant.