Climate Commons^™

Pyseqrna: An Automated Python Package For Advanced Rna Sequencing Data Analysis And Annotation, Naveen Duhan

Student Research Symposium

Abstract: With the advent of Next-Generation Sequencing (NGS) technologies, numerous data is being generated every day, however, streamlined analysis remains a big hurdle to efficiently use the technology. A large number of algorithms, statistical methods, and software tools have been developed in recent years to perform the individual analysis steps of various NGS applications. Some NGS applications data analysis procedures are therefore very complex, requiring several program tools to be downloaded for their various processing steps. There is a significant room for the development of scalable computing environments that link the individual software components to automated workflows to efficiently and …

Deepnec: A Novel Alignment-Free Tool For The Characterization Of Nitrification-Related Enzymes Using Deep Learning, A Step Towards Comprehensive Understanding Of The Nitrogen Cycle, Naveen Duhan

Student Research Symposium

Abstract: Nitrification is an important microbial two-step transformation in the global nitrogen cycle, as it is the only natural process that produces nitrate within a system. The functional annotation of nitrification-related enzymes has a broad range of applications in metagenomics, agriculture, industrial biotechnology, etc. The time and resources needed for determining the function of enzymes experimentally are restrictively costly. Therefore, an accurate genome-scale computational prediction of the nitrification-related enzymes has become much more important.In this study, we developed an alignment-free computational approach to determine the nitrification-related enzymes from the sequence itself. We propose deepNEC, a novel end-to-end feature selection and …

Nitrogen Use Efficiency And Soil Bioavailable Nitrogen In Corn Silage Production In A Semi-Arid Environment, Phearen Miller

Student Research Symposium

As agriculture intensifies, the world faces a dual challenge of increasing food production while reducing impacts of excess reactive nitrogen (N) in the environment. A field study examining different N sources in corn silage under semi-arid conditions was conducted at the Greenville farm in northern Utah (41°45’ N, 1111°48’52 W) since 2012. The experimental design is a randomized complete block design with four blocks and four treatments: control (no nitrogen), low ammonium sulfate (AS 112 kg N/ha), high ammonium sulfate (AS 224 kg N/ha), and steer manure compost (224 kg total N/ha). We examined yield, nitrogen use efficiency (NUE), and …

A Stratospheric Approach To Diagnose The North American Winter Dipole, Henrik Panosyan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

It has been well established in the literature that the stratosphere is dynamically coupled with the troposphere during boreal winter. The North American Winter Dipole is comprised of an upper-tropospheric contrast between a ridge over western North America, and a trough over eastern North America. The variance of this circulation regime has increased in recent years, with its amplified states being associated with extremes ranging from drought and floods, to extreme cold air outbreaks. This study explores the stratospheric link to this extreme weather regime, in the hopes of ultimately improving the predictability of this regime on intraseasonal-to-seasonal timescales. We …

Pacific Decadal Oscillation Remotely Forced By The Equatorial Pacific And The Atlantic Oceans, Zachary F. Johnson, Yoshimitsu Chikamoto, Shih-Yu Simon Wang, Michael J. Mcphaden, Takashi Mochizuki

Plants, Soils, and Climate Faculty Publications

The Pacific Decadal Oscillation (PDO), the leading mode of Pacific decadal sea surface temperature variability, arises mainly from combinations of regional air-sea interaction within the North Pacific Ocean and remote forcing, such as from the tropical Pacific and the Atlantic. Because of such a combination of mechanisms, a question remains as to how much PDO variability originates from these regions. To better understand PDO variability, the equatorial Pacific and the Atlantic impacts on the PDO are examined using several 3-dimensional partial ocean data assimilation experiments conducted with two global climate models: the CESM1.0 and MIROC3.2m. In these partial assimilation experiments, …

Change In The Leading Mode Of North America's Wintertime Stationary Eddies, Yu-Tang Chien

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Extreme winter weather events in North America have become more frequent and increasingly destructive. This phenomenon was linked to a jet stream pattern that generates abnormally warm conditions in the west and cold conditions in the east, referred to as the North American Winter Dipole. Studies have shown that the Dipole may have amplified and this amplification could be linked to global warming. By analyzing the atmospheric and oceanic data worldwide, the wintertime circulation in the Northern Hemisphere shows signs of a persistent change after the 1980s. In the first part of this study, we examine how the ocean has …

Intermittent Turbulent Exchanges And Their Role In Vineyard Evapotranspiration, Sebastian Alexander Los

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Vineyards are often grown in semi-arid climates, such as California’s central valley, where water resources can be limited. Summer weather conditions result in high water use by these plants. For wine grapes, a high-value commodity, there are known benefits to fruit quality in irrigating grapevines with slightly below optimum for the plant. Growers would like to be able to precisely irrigate without overusing water or overstressing the vines. This calls for improving ways to monitor vineyard water use by estimating the combined soil evaporation and plant transpiration known as evapotranspiration (ET). A computer model developed by the USDA called the …

Phosphorus Rate Effects With And Without Avail® On Dryland Winter Wheat In An Eroded Calcareous Soil, Ryan C. Hodges

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Soluble phosphorus fertilizer is bound in the soil rapidly after application in soils high in calcium. A fertilizer additive known as AVAIL® (J.R. Simplot Company) is purported to keep applied phosphorus fertilizer more available to plants by binding to soil minerals such as calcium, magnesium, and iron, thereby reducing phosphorus binding. This could prove useful due to the attraction of AVAIL® with cations such as Ca²⁺, but is fairly unstudied for dryland wheat production on alkaline, calcium-rich soils. The objective of this study is to evaluate the effect of low-rate fertilizer treatments with AVAIL® on dryland small grain …

Creative Citizen Science Illuminates Complex Ecological Responses To Climate Change, Abraham J. Miller-Rushing, Amanda S. Gallinat, Richard B. Primack

Biology Faculty Publications

Climate change is causing the timing of key behaviors (i.e., phenology) to shift differently across trophic levels and among some interacting organisms (e.g., plants and pollinators, predators and prey), suggesting that interactions among species are being disrupted (1, 2). Studying the phenology of interactions, however, is difficult, which has limited researchers’ ability to zero in on changes in specific interactions or on the consequences of mismatches. In PNAS, Hassall et al. (3) use a combination of citizen science techniques to investigate the effects of climate change on dozens of specific interactions. They focus on a Batesian mimicry complex involving stinging …

The Influence Of Arctic Amplification On Mid-Latitude Summer Circulation, Dim Coumou, Giorgia Di Capua, Steve Vavrus, Lei Wang, Shih-Yu (Simon) Wang

Plants, Soils, and Climate Faculty Publications

Accelerated warming in the Arctic, as compared to the rest of the globe, might have profound impacts on mid-latitude weather. Most studies analyzing Arctic links to mid-latitude weather focused on winter, yet recent summers have seen strong reductions in sea-ice extent and snow cover, a weakened equator-to-pole thermal gradient and associated weakening of the mid-latitude circulation. We review the scientific evidence behind three leading hypotheses on the influence of Arctic changes on mid-latitude summer weather: Weakened storm tracks, shifted jet streams, and amplified quasi-stationary waves. We show that interactions between Arctic teleconnections and other remote and regional feedback processes could …

Natural And Managed Watersheds Show Similar Responses To Recent Climate Change, Darren L. Ficklin, John T. Abatzoglou, Scott M. Robeson, Sarah E. Null, Jason H. Knouft

Watershed Sciences Faculty Publications

Changes in climate are driving an intensification of the hydrologic cycle and leading to alterations of natural streamflow regimes. Human disturbances such as dams, land-cover change, and water diversions are thought to obscure climate signals in hydrologic systems. As a result, most studies of changing hydroclimatic conditions are limited to areas with natural streamflow. Here, we compare trends in observed streamflow from natural and human-modified watersheds in the United States and Canada for the 1981–2015 water years to evaluate whether comparable responses to climate change are present in both systems. We find that patterns and magnitudes of trends in median …

Influence Of Global Atmospheric Circulation Variations On Weather And Climate Extremes, Yen-Heng Lin

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Global warming and climate change deeply influence weather and climate extremes, causing substantial property damage and loss every year around the world. Given the importance of heating differences between low-latitude and Arctic regions, which produce heat sources and cold sources that each influence global circulations, we investigate three extreme weather events in different regions in order to better understand the possible connections between extreme events and global circulation changes.

This study begins with climate variations in the low-latitude western North Pacific. In early summer, the timing of the wet season has shifted from late May to early June since 1979. …

Towards The Prediction Of Climate Extremes With Attribution Analysis Through Climate Diagnostics And Modeling: Cases From Asia To North America, Boniface Opoku Fosu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This project summarizes the findings of research organized in two parts. The first involved the characterization of changes in the variability of climate that lead to extreme events. The second focused on the predictability of extreme climate on time-scales ranging from short forecast lead-times to long-lead climate predictions exceeding a year.

Initial studies focused on three interrelated, yet regionally unique extreme climate phenomena. First, the relationship between increasing greenhouse gas (GHG) emissions and particulate matter (PM) concentration in basin terrain was investigated. Next, we evaluated changes in large-scale atmospheric circulation associated with two climate phenomena at either extreme side of …

Regional Trends In Early-Monsoon Rainfall Over Vietnam And Ccsm4 Attribution, Rong Li, S.-Y. Simon Wang, Robert R. Gillies, Brendan Buckley, Jin-Ho Yoon, Changrae Cho

Plants, Soils, and Climate Faculty Publications

The analysis of precipitation trends for Vietnam revealed that early-monsoon precipitation has increased over the past three decades but to varying degrees over the northern, central and southern portions of the country. Upon investigation, it was found that the change in early-monsoon precipitation is associated with changes in the low-level cyclonic airflow over the South China Sea and Indochina that is embedded in the large-scale atmospheric circulation associated with a “La Niña-like” anomalous sea surface temperature pattern with warming in the western Pacific and Indian Oceans and cooling in the eastern Pacific. The Community Climate System Model version 4 (CCSM4) …

Multidecadal Variability In The Subseasonal Peak Of Low-Level Convergence Over The Pacific Warm Pool, Yen-Heng Lin, Shih-Yu (Simon) Wang

Plants, Soils, and Climate Faculty Publications

In the Western North Pacific (WNP), the atmospheric low-level convergence is one of the main factors that influences the genesis of tropical cyclones (TC). It has been observed that the timing of the seasonal maxima in the low-level convergence and TC genesis has shifted since the mid-1990s from mid-August to late-July, with this shift having also affected the number of TC. A multidecadal frequency of 20 years was revealed in the timing variation of the tropical intraseasonal oscillation (ISO) in the Western Pacific, in which a weak WNP low-level convergence in spring may trigger an advanced ISO phase in summer …

Non-Methane Hydrocarbon Source Apportionment And Btex Risk Assessment Of Winter 2015 In Roosevelt, Utah, Jerimiah Lamb

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Non-Methane Hydrocarbons (NMHC) monitored in Roosevelt Utah including Benzene, Toluene, Ethylbenzene and Xylene (collectively known as BTEX) are associated with deleterious effects including cancer. This study was designed to assess the origin and effect of the toxicants and addressed two points: 1) Source identification using the USEPA’s Positive Matrix Factorization (PMF) and NOAA’s Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model and 2) A human health risk assessment based on ambient concentrations of BTEX collected at the Roosevelt site. Model fit indicated that the primary contributor to total NMHCs was local oil and gas operations and was supported by previous …

Apathy And Concern Over The Future Habitability Of Earth: An Introductory College Assignment Of Forecasting Co2 In The Earth’S Atmosphere, Benjamin J. Burger

Journal on Empowering Teaching Excellence

Non-science, first year regional undergraduate students from rural Utah communities participated in an online introductory geology course and were asked to forecast the rise of CO₂ in the Earth’s atmosphere. The majority of students predicted catastrophic rise to 5,000-ppm sometime over the next 3,100 years, resulting in an atmosphere nearly uninhabitable to human life. However, the level of concern the students exhibited in their answers was not directly proportional with their timing in their forecasted rise of CO₂. This study showcases the importance of presenting students with actual data and using data to develop student forecasted models. …

Modeling And Projection Of The North American Monsoon Using A High-Resolution Regional Climate Model, Jonathan D.D. Meyer

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The North American Monsoon (NAM) is a dominant climate feature across the southwestern United States and Mexico during the summertime. Rainfall from the NAM elicits a significant response from the regional ecology as well as supports the socioeconomic well-being of both rural and urban populations. Due to the large variability in the yearly intensity and location of where the NAM rainfall occurs, the region is highly susceptible to prolonged and exceptional periods of drought; compounded by significant population growth projections through the 21st century. Reliable prediction for the NAM is highly beneficial on timescales ranging from shortterm weather forecasting to …

Gridded Snow Water Equivalent Reconstruction For Utah Using Forest Inventory And Analysis Tree-Ring Data, Daniel Barandiaran, Shih-Yu (Simon) Wang, R. Justin Derose

Plants, Soils, and Climate Faculty Publications

Snowpack observations in the Intermountain West are sparse and short, making them difficult for use in depicting past variability and extremes. This study presents a reconstruction of April 1 snow water equivalent (SWE) for the period of 1850–1989 using increment cores collected by the U.S. Forest Service, Interior West Forest Inventory and Analysis program (FIA). In the state of Utah, SWE was reconstructed for 38 snow course locations using a combination of standardized tree-ring indices derived from both FIA increment cores and publicly available tree-ring chronologies. These individual reconstructions were then interpolated to a 4-km grid using an objective analysis …

Future Changes In Propagating And Non-Propagating Diurnal Rainfall Over East Asia, Wan-Ru Huang, Shih-Yu (Simon) Wang

Plants, Soils, and Climate Faculty Publications

The characteristics of diurnal rainfall in the East Asian continent consist of a propagating regime over the Yangtze River and a non-propagating regime in southeast China. Simulations of these two diurnal rainfall regimes by 18 CMIP5 models were evaluated from the historical experiment of 1981–2005. The evaluation led to the identification of one model, the CMCC-CM that replicated the key characteristics of diurnal rainfall regimes including the propagation of moisture convergence. Using the CMCC-CM to assess the future (2076–2100) change of diurnal evolution and propagation projected by the RCP4.5 experiment, it was found that propagating diurnal rainfall will enhance and …

Investigation Into Regional Climate Variability Using Tree-Ring Reconstruction, Climate Diagnostics And Prediction, Daniel A. Barandiaran

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This document summarizes research conducted to develop and apply climate analysis tools toward a better understanding of the past and future of climate variability in the state of Utah. Two pilot studies developed analysis tools through the investigation of natural variability in precipitation systems in Africa, and research into long-term changes and trends in spring rainfall over the U.S. Great Plains. Our third study used tree-ring data to estimate snowpack in the state of Utah to 1850, doubling the length of record and offering a better understanding of the history of snowpack in the state. Our final study looked at …

Role Of The Strengthened El Nino Teleconnection In The May 2015 Floods Over The Southern Great Plains, S.-Y. Wang, W.-R. Huang, H.-H. Hsu, R. R. Gillies

Plants, Soils, and Climate Faculty Publications

The climate anomalies leading to the May 2015 floods in Texas and Oklahoma were analyzed in the context of El Niño teleconnection in a warmer climate. A developing El Niño tends to increase late-spring precipitation in the southern Great Plains, and this effect has intensified since 1980. Anthropogenic global warming contributed to the physical processes that caused the persistent precipitation in May 2015: Warming in the tropical Pacific acted to strengthen the teleconnection toward North America, modification of zonal wave 5 circulation that deepened the stationary trough west of Texas, and enhanced Great Plains low-level southerlies increasing moisture supply from …

The 2011 Great Flood In Thailand: Climate Diagnostics And Implications From Climate Change, Parichart Promchote, S. -Y. Simon Wang, Paul G. Johnson

Plants, Soils, and Climate Faculty Publications

Severe flooding occurred in Thailand during the 2011 summer season, which resulted in more than 800 deaths and affected 13.6 million people. The unprecedented nature of this flood in the Chao Phraya River basin (CPRB) was examined and compared with historical flood years. Climate diagnostics were conducted to understand the meteorological conditions and climate forcing that led to the magnitude and duration of this flood. Neither the monsoon rainfall nor the tropical cyclone frequency anomalies alone was sufficient to cause the 2011 flooding event. Instead, a series of abnormal conditions collectively contributed to the intensity of the 2011 flood: anomalously …

The North American Winter 'Dipole' And Extremes Activity: A Cmip5 Assessment, Shih-Yu (Simon) Wang, Wan-Ru Huang, Jin-Ho Yoon

Plants, Soils, and Climate Faculty Publications

The 2013–2014 winter in North America brought intense drought in the West and severe cold in the East. The circulation anomalies were characterized as a dipole: an amplified upper-level ridge over the West Coast and a deepened trough over the central-eastern United States. A previous study using a single model has linked the dipole to the El Niño precursor and found that this link has strengthened in recent years. Here, 17 models from the Coupled Model Intercomparison Project Phase 5 are used to examine the dipole activity. Most models capture the dipole and its association with El Niño precursor and …

A Combined Dynamical And Statistical Downscaling Technique To Reduce Biases In Climate Projections: An Example For Winter Precipitation And Snowpack In The Western United States, R. Li, Shih-Yu (Simon) Wang, R. R. Gillies

Plants, Soils, and Climate Faculty Publications

Large biases associated with climate projections are problematic when it comes to their regional application in the assessment of water resources and ecosystems. Here, we demonstrate a method that can reduce systematic biases in regional climate projections. The global and regional climate models employed to demonstrate the technique are the Community Climate System Model (CCSM)and the Weather Research and Forecasting (WRF) model. The method first utilized a statistical regression technique and a global reanalysis dataset to correct biases in the CCSM-simulated variables (e.g., temperature, geopotential height, specific humidity, and winds) that are subsequently used to drive the WRF model. …

Decadal Oscillation Of Autumn Precipitation In Central Vietnam Modulated By The East Pacific-North Pacific (Ep-Np), R. Li, Shih-Yu (Simon) Wang, R. R. Gillies, B. Buckley, L. H. Troung, C. Cho

Plants, Soils, and Climate Faculty Publications

Autumn precipitation over Central Vietnam is associated with an increase in the occurrence of tropical cyclones that lead to frequent flooding and pose a significant threat to lives and property. The present analyses reveal a pronounced decadal oscillation of autumn precipitation in Central Vietnam within the 8-11 year frequency band that is modulated by the East Pacific-North Pacific (EP-NP) teleconnection. The negative phase of the EP-NP pattern is associated with a positive sea surface temperature (SST) anomaly in the South China Sea (SCS) that induces low-level convergence, enhances convection, and increases precipitation over Central Vietnam and adjacent islands including Hainan …

Anthropogenic Footprint Of Climate Change In The June 2013 Northern India Flood, C. Cho, R. Li, Shih-Yu (Simon) Wang, J. -H. Yoon, R. R. Gillies

Plants, Soils, and Climate Faculty Publications

During 13-17 June 2013, heavy rainfall occurred in the northern Indian state of 15 Uttarakhand and led to one of the worst floods in history and massive landslides, 16 resulting in more than 5,000 casualties and a huge loss of property. In this study, 17 meteorological and climatic conditions leading up to this rainfall event in 2013 and 18 similar cases were analyzed for the period of 1979-2012. Attribution analysis was 19 performed to identify the natural and anthropogenic influences on the climate anomalies 20 using the historical single-forcing experiments in the Coupled Model Intercomparison 21 Project Phase 5 (CMIP5). …

Observing The Quantumbehavior Of Light In An Undergraduate Laboratory, M. S. Neel, J. J. Thorn, V. W. Donato, G. S. Bergreen, Robert E. Davies, M. Beck

Plants, Soils, and Climate Faculty Publications

While the classical, wavelike behavior of light (interference and diffraction) has been easily observed in undergraduate laboratories for many years, explicit observation of the quantum nature of light (i.e., photons) is much more difficult. For example, while well-known phenomena such as the photoelectric effect and Compton scattering strongly suggest the existence of photons, they are not definitive proof of their existence. Here we present an experiment, suitable for an undergraduate laboratory, that unequivocally demonstrates the quantum nature of light. Spontaneously downconverted light is incident on a beamsplitter and the outputs are monitored with single-photon counting detectors. We observe a near …

Probable Causes Of The Abnormal Ridge Accompanying The 2013-14 California Drought: Enso Precursor And Anthropogenic Warming Footprint, Shih-Yu (Simon) Wang

Plants, Soils, and Climate Faculty Publications

The 2013–2014 California drought was initiated by an anomalous high-amplitude ridge system. The anomalous ridge was investigated using reanalysis data and the Community Earth System Model (CESM). It was found that the ridge emerged from continual sources of Rossby wave energy in the western North Pacific starting in late summer and subsequently intensified into winter. The ridge generated a surge of wave energy downwind and deepened further the trough over the northeast U.S., forming a dipole. The dipole and associated circulation pattern is not linked directly with either El Niño–Southern Oscillation (ENSO) or Pacific Decadal Oscillation; instead, it is correlated …

Climate Forcings On Groundwater Variations In Utah And The Great Basin, Kirsti A. Hakala

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Groundwater levels over northern Utah have undergone a declining trend since the 1960’s. This trend has made apparent the need to understand the relationship between climate and groundwater resources. Such necessary information is already in dire need in places such as California. At the close of 2013, California had experienced its driest year in recorded history, with severe drought continuing for the foreseeable future. Utah is the second driest state in the U.S., and therefore has been paying close attention to California’s current water crises. Water resource projections may prove to be one of the most vital pieces of information …