Life Sciences Commons^™

2013 - Greater Monterey County Integrated Regional Water Management - Disadvantaged Community And Tribal Needs Assessment

Miscellaneous Monterey and San Luis Obispo County Documents and Reports

A 2013 Disadvantaged Community and Tribal Needs Assessment as they relate to water management in the Greater Monterey County Integrated Regional Water Management process in the planning region thus informing future project development.

Als Mutations Of Fus Suppress Protein Translation And Disrupt The Regulation Of Nonsense-Mediated Decay, Marisa Kamelgarn, Jing Chen, Lisha Kuang, Huan Jin, Edward J. Kasarskis, Haining Zhu

Toxicology and Cancer Biology Faculty Publications

Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease characterized by preferential motor neuron death. Approximately 15% of ALS cases are familial, and mutations in the fused in sarcoma (FUS) gene contribute to a subset of familial ALS cases. FUS is a multifunctional protein participating in many RNA metabolism pathways. ALS-linked mutations cause a liquid–liquid phase separation of FUS protein in vitro, inducing the formation of cytoplasmic granules and inclusions. However, it remains elusive what other proteins are sequestered into the inclusions and how such a process leads to neuronal dysfunction and degeneration. In this study, we developed …

The Evolution Of Diet Breadth In Melissodes Bees (Apidae: Eucerini), Karen W. Wright

Biology ETDs

The relationship between phytophagous insects and their host plants has interested scientists since Darwinian times. Using modern phylogenetic inference, we are able to investigate these patterns using, not only the phylogenies of the insects, but the evolutionary relationships among the plants they feed on as well. The relationships between bees and the plants they pollinate were traditionally seen as mutualistic and were treated separately from the research investigating the antagonistic relationships between phytophagous insects and their host plants. However, recent phylogenetic studies have made great progress including bee-host relationships in with the larger body of work on phytophagous insects.

The …

Spoil Type Influences Soil Genesis And Forest Development On An Appalachian Surface Coal Mine Ten Years After Placement, Kenton L. Sena, Carmen T. Agouridis, Jarrod Miller, Christopher D. Barton

Lewis Honors College Faculty Publications

Surface mining for coal (or other mineral resources) is a major driver of land-use change around the world and especially in the Appalachian region of the United States. Intentional and well-informed reclamation of surface-mined land is critical for the restoration of healthy ecosystems on these disturbed sites. In Appalachia, the pre-mining land cover is predominately mixed hardwood forest, with rich species diversity. In recent years, Appalachian mine reforestation has become an issue of concern, prompting the development of the Forestry Reclamation Approach, a series of mine reforestation recommendations. One of these recommendations is to use the best available soil substitute; …

Mrna, Rrna And Dna Quantitative Stable Isotope Probing With H218o Indicates Use Of Old Rrna Among Soil Thaumarchaeota, Katrina Papp, Bruce A. Hungate, Egbert Schwartz

Civil and Environmental Engineering and Construction Faculty Research

RNA is considered to be a short-lived molecule, indicative of cellular metabolic activity, whereas DNA is thoughtto turn over more slowly because living cells do not always grow and divide. To explore differences in the ratesof synthesis of these nucleic acids, we used H218O quantitative stable isotope probing (qSIP) to measure theincorporation of18O into 16S rRNA, the 16S rDNA,amoAmRNA and theamoAgene of soil Thaumarchaeota.Incorporation of18O into the thaumarchaealamoAmRNA pool was faster than into the 16S rRNA pool,suggesting that Thaumarchaea were metabolically active while using rRNA molecules that were likely synthe-tized prior to H218O addition. Assimilation rates of18O into 16S rDNA …

Effects Of Urbanization On The Foraging Ecology And Microbiota Of The Generalist Seabird Larus Argentatus, Matthew Fuirst, Richard R. Veit, Megan Hahn, Nolwenn Dheilly, Lesley H. Thorne

Publications and Research

Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. …

2014 - Quarternary Geologic Map Of North-Central Salinas River Valley And Arroyo Seco

Miscellaneous Monterey and San Luis Obispo County Documents and Reports

The new mapping provides a detailed stratigraphic history of incision and deposition from the early Pleistocene to the present. Infiltration from the Salinas River and its tributaries is the source of irrigation water in this agricultural region. Irrigation water is pumped from the aquifers at depths of about 55 and 120 m. Area has become intruded by seawater, especially between cities of Castroville and Salinas.

Repeats Of Unusual Size In Plant Mitochondrial Genomes: Identification, Incidence And Evolution, Emily L. Wynn, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are …

Proteomic Profile Of Carbonylated Proteins Screen Regulation Of Apoptosis Via Camk Signaling In Response To Regular Aerobic Exercise, Wenfeng Liu, Li Li, Heyu Kuang, Yan Xia, Zhiyuan Wang, Shaopeng Liu, Dazhong Yin

Health Sciences & Kinesiology: Faculty Publications

To research carbonylated proteins and screen molecular targets in the rat striatum on regular aerobic exercise, male SpragueDawley rats (13 months old, n = 24) were randomly divided into middle-aged sedentary control (M-SED) and aerobic exercise (M-EX) groups (n = 12 each). Maximum oxygen consumption (VO2max) gradually increased from 50%–55% to 65%–70% for a total of 10 weeks. A total of 36 carbonylated proteins with modifed oxidative sites were identifed by Electrospray IonizationQuadrupole-Time of Flight-Mass Spectrometer (ESI-Q-TOF-MS), including 17 carbonylated proteins unique to the M-SED group, calcium/calmodulin-dependent protein kinase type II subunit beta (CaMKII�), and heterogeneous nuclear ribonucleoprotein A2/B1 (Hnrnpa2b1), …

Revision Of The Central Asian Scorpion Genus Anomalobuthus Kraepelin, 1900, With Descriptions Of Three New Species And A Generic Synonymy (Scorpiones: Buthidae), Rolando Teruel, František Kovařík, Victor Fet

Euscorpius

We revise the Central Asian endemic genus Anomalobuthus Kraepelin, 1900, which was considered monotypic for more than 100 years until the recent addition of a second species from Iran (Teruel et al., 2014). We redefine the generic diagnosis of Anomalobuthus and reveal that it is composed of no less than six species, three of which are described as new: A. krivochatskyi, sp. n. (central Uzbekistan and extreme southern Kazakhstan), A. lowei, sp. n. (southeastern Kazakhstan), and A. pavlovskyi, sp. n. (south-central Kazakhstan and extreme northern Turkmenistan). The monotypic genus Psammobuthus Birula, 1911 (described from the Ferghana Valley …

Minimum Information About An Uncultivated Virus Genome (Miuvig), Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A. Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, François Enault, Jed A. Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalie N. Ivanova, Jessica M. Labonté, Kyung-Bum Lee, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster, Katrine L. Whiteson, Steven W. Whilhelm, K Eric Wommack, Tanja Woyke, Kelly C. Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh

Bioinformatics Faculty Publications

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative …

Dependence Of Aspen Stands On A Subsurface Water Subsidy: Implications For Climate Change Impacts, D. M. Love, M. D. Venturas, J. S. Sperry, P. D. Brooks, J. L. Pettit, Y. Wang, W. R. L. Anderegg, X. Tai, D. S. Mackay

Aspen Bibliography

The reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait- and process-based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and …

Pasnet: Pathway-Associated Sparse Deepneural Network For Prognosis Prediction From High-Throughput Data, Jie Hao, Youngsoon Kim, Tae-Kyung Kim, Mingon Kang

Faculty Articles

Background: Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis maybe caused by high complexity of biological systems, where multiple biological components and their hierarchical relationships are involved. Moreover, it is challenging to develop robust computational solutions with high-dimension, low-sample size data. Results: In this study, we propose a Pathway-Associated Sparse Deep Neural Network (PASNet) that not only predicts patients’ prognoses but also describes complex biological processes regarding biological pathways for prognosis. PASNet models a multilayered, hierarchical biological system of genes …

Dependence Of Aspen Stands On A Subsurface Water Subsidy: Implications For Climate Change Impacts, D. M. Love, M. D. Venturas, J. S. Sperry, P. D. Brooks, Joseph L. Pettit, Y. Wang, W. R.L. Anderegg, X. Tai, D. S. Mackay

Wildland Resources Faculty Publications

The reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait‐ and process‐based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and …

Engineering Eden: The World's Attempt To Outsmart Water Scarcity, Kaitlin A. Sullivan

Capstones

Countries around the world are running out of fresh water, 43 already live with water scarcity, requiring more water than they have. In 2015 the global water crisis took first place in The World Economic Forum’s assessment of the risks that will have the most significant impact on economies, environments and people. Water beat out 27 other long-term risks including infectious diseases and weapons of mass destruction. What happened to Crowley County on the plains of Southeastern Colorado is a cautionary tale of borrowed water. It's been called the Detroit of Colorado, decimated by the reliance of a single industry. …

The Invisible Brain Injury Crisis, Michael E. Rosenthal

Capstones

According to the Center for Disease Control and Prevention’s 2013 data, over 282,000 hospitalizations and 2.5 million emergency department visits were at least in part attributable to TBI. In the same year, about 56,000 people died.

Emergency departments in 2012 treated about 329,290 kids under 20 for TBI following an injury taking place during physical activity.

This project explores the rise in traumatic brain injuries and examines the difficult path that some of the survivors have to go through during recovery. By telling the story through my own personal experiences, I guide the reader through what the initial trauma and …

Life History And Habitat Of The Rare Patch-Nosed Salamander (Urspelerpes Brucei), Carlos D. Camp, Tyler L. Brock, Todd W. Pierson, Joseph Milanovich, John C. Maerz

Biology: Faculty Publications and Other Works

We examined the life history and habitat characteristics for the Patch-nosed Salamander, Urspelerpes brucei. Body-size measurements of individuals captured using litter bags and by hand from 2008 to 2010 indicated that the larval period lasts at least 2 y, salamanders attain reproductive maturity at or shortly after metamorphosis, and adults have very little variation in body size. Occupied streams are characterized by small size, little water, and narrow, steep-walled ravines. Within occupied streams, larval capture rate was significantly and negatively related to mean water depth, underscoring the importance of protecting headwaters. We hypothesize that the only known population of U. …

The Effects Of A 12-Week Jump Rope Exercise Program On Abdominal Adiposity, Vasoactive Substances, Inflammation, And Vascular Function In Adolescent Girls With Prehypertension, Ki-Dong Sung, Elizabeth J. Pekas, Steven D. Scott, Won-Mok Son, Song-Young Park

Health and Kinesiology Faculty Publications

Introduction

Childhood obesity is strongly associated with cardiovascular disease (CVD) development. It is necessary to combat unfavorable outcomes of obesity at a young age by utilizing effective interventions, such as exercise.

Purpose

We sought to examine the effects of a jump rope exercise program on CVD risk factors, including body composition, vasoactive substances, inflammation, and vascular function in prehypertensive adolescent girls.

Methods

Forty girls (age 14–16) were recruited and randomly assigned to a jump rope exercise group (EX, n = 20) or control group (CON, n = 20). Body composition, nitrate and nitrite levels, endothelin-1 (ET-1), C-reactive protein (CRP), systolic …

Antibiofilm Activities Of Extracts Of The Macroalga Halimeda Sp. From The Red Sea, Alaa Aref Abdullah Gadhi, Mohsen M. O El-Sherbiny, Abdul Mohsin A Al-Sofyani, Mohammad Abdulaziz Ba-Akdah, Sathianeson Satheesh

Journal of Marine Science and Technology–Taiwan

Marine macroalgae generally keep their surface free from fouling organisms by their antifouling defence. Antifouling activity has been attributed to the production of secondary metabolites. In the present study, antifouling performance of the macroalga Halimeda sp., collected from the Red Sea coastal waters, was assessed using extracts prepared through various methods, including surface extraction, wet sample extraction and dried sample extraction. The solvents methanol and hexane were used to assess the effect of solvents on bioactivity. Results indicated that extracts of the macroalga inhibited growth and settlement of a biofilm-forming bacterial strain. Though the extracts prepared using different methods and …

Grammar And Variation: Understanding How Cis-Regulatory Information Is Encoded In Mammalian Genomes, Dana Michele King

Arts & Sciences Graduate Student Theses and Dissertations

Understanding how genotype leads to phenotype is key to understand both the development and dysfunction of complex organisms. In the context of regulating the gene expression patterns that contribute to cell identity and function, the goal of my thesis research is to how changes in genome sequence may impact impact gene expression by determining how sequence features contribute to regulatory potential. To accomplish this goal, I first leveraged the key regulatory role of pluripotency transcription factors (TFs) in mouse embryonic stem cells (mESCs) and tested synthetically generated and genomic identified combinations of binding site for four TFs, OCT4, SOX2, KLF4, …

Fast Objective Coupled Planar Illumination Microscopy, Cody Jonathan Greer

Arts & Sciences Graduate Student Theses and Dissertations

Among optical imaging techniques light sheet fluorescence microscopy stands out as one of the most attractive for capturing high-speed biological dynamics unfolding in three dimensions. The technique is potentially millions of times faster than point-scanning techniques such as two-photon microscopy. This potential is especially poignant for neuroscience applications due to the fact that interactions between neurons transpire over mere milliseconds within tissue volumes spanning hundreds of cubic microns. However current-generation light sheet microscopes are limited by volume scanning rate and/or camera frame rate. We begin by reviewing the optical principles underlying light sheet fluorescence microscopy and the origin of these …

The Splice Is Not Right: Splice-Site-Creating Mutations In Cancer Genomes, Reyka Glencora Jayasinghe

Arts & Sciences Graduate Student Theses and Dissertations

Accurate interpretation of cancer mutations in individual tumors is a prerequisite for precision medicine. Large-scale sequencing studies, such as The Cancer Genome Atlas (TCGA) project, have worked to address the functional consequences of genomic mutations, with the larger goal of determining the underlying mechanisms of cancer initiation and progression. Many studies have focused on characterizing non-synonymous somatic mutations that alter amino acid sequence, as well as splice disrupting mutations at splice donors and acceptors. Current annotation methods typically classify mutations as disruptors of splicing if they fall on the consensus intronic dinucleotide splice donor, GT, the splice acceptor, AG. Splice …

Modeling The Bioactivation And Subsequent Reactivity Of Drugs, Tyler Brian Hughes

Arts & Sciences Graduate Student Theses and Dissertations

Metabolism can convert drugs to harmful reactive metabolites that conjugate to DNA and off-target proteins. Reactive metabolites are a significant driver of both drug candidate attrition and withdrawal from the market of already approved drugs. Unfortunately, reactive metabolites are difficult to study in vivo, because they are transitory and generally do not circulate. Instead, this work computationally models both metabolism and reactivity. Using deep learning, predictive models were developed for the metabolic formation of quinones and epoxides, which together account for about half of known reactive metabolites. Additionally, an accurate model of DNA and protein reactivity was constructed, which predicts …

Protein Structure-Guided Approaches To Identify Functional Mutations In Cancer, Sohini Sengupta

Arts & Sciences Graduate Student Theses and Dissertations

Distinguishing driver mutations from passenger mutations within tumor cells continues to be a major challenge in cancer genomics. Many computational tools have been developed to address this challenge; however, they rely heavily on primary protein sequence context and frequency/mutation rate. Rare driver mutations not found in many cancer patients may be missed with these traditional approaches. Additionally, the structural context of mutations on tertiary/quaternary protein structures is not taken into account and may play a more prominent role in determining phenotype and function. This dissertation first presents a novel computational tool called HotSpot3D, which identifies regions of protein structures that …

Effects Of Ambient Air Pollution On Asthma-Related Emergency Department Visits Within The Las Vegas Metropolitan Area, Loiren E. Monardes

UNLV Theses, Dissertations, Professional Papers, and Capstones

The objective of this research was to evaluate the risk for asthma-related Emergency Department visits and their association with ambient air pollution within the Las Vegas metropolitan area. All data were aggregated by date and ZIP Code. The association was analyzed by applying the distributed lag non-linear model in an attempt to identify elevated concentrations of specific air pollutants

as triggers and their delayed effects (lag days). Relative Risk (RR) and 95% confidence intervals were produced, while adjusting for socioeconomic status. This ecological population-based study analyzed daily asthma counts of Emergency Department visits from January 1st, 2009 to December 31st, …

Riding The Wave Of Microplastics In Bermuda, Molly E. Riihiluoma

Pell Scholars and Senior Theses

The presence of marine debris and microplastics in the Earth’s oceans are a global environmental issue. Bermuda’s location in the middle of the North Atlantic Gyre makes it the perfect case study for this work. As the crisis unfolds, Bermuda’s environment, economy, and population are at risk of witnessing firsthand the effects of plastic pollution. This paper relies on scholarly research as well as anecdotal evidence from retail stores and locals to compile information in order to provide necessary recommendations to benefit Bermuda’s ocean health. This research evaluates the pros and cons of policies which could mitigate the problem. Analysis …

Establishment Of Turfgrass From Seed And Sod In Sand Based Systems Combining Sprinkler And Subsurface Drip Irrigation Systems, Roshaan Ahmed Khan Niazi

Electronic Theses and Dissertations

The establishment of turfgrass using subsurface drip irrigation (SDI) in sand based media has limited success. However, it is unknown if starting with overhead (sprinkler) irrigation and transitioning to SDI can enhance turfgrass establishment. Two experiments were conducted at Stephen F. Austin State University (SFASU) to investigate the establishment of “L-93” creeping bentgrass (Agrostis stolonifera) from seed and “TifEagle” ultra dwarf hybrid bermudagrass (Cynodon dactylon x Cynodon transvaalensis) from sod using sand based media. Each experiment consisted of two trials conducted in summer 2017 and spring 2018. Both creeping bentgrass trials and the spring ultra dwarf …

A Force Sensor That Converts Fluorescence Signal Into Force Measurement Utilizing Short Looped Dna, Golam Mustafa, Cho-Ying Chuang, William A. Roy, Mohamed M. Farhath, Nilisha Pokhrel, Yue Ma, Kazuo Nagawawa, Edwin Antony, Matthew J. Comstock, Soumitra Basu, Hamza Balci

Biological Sciences Faculty Research and Publications

A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged …

Kcnq1/Kcne1 Interaction In The Cardiac Iks Channel And Its Physiological Consequences, Jiajing Xu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Dynamic conformational changes of ion channel proteins during activation gating determine their function as carriers of current. The relationship between these molecular movements and channel function over the physiological timescale of the action potential (AP) has not been fully established due to limitations of existing techniques. We constructed a library of possible cardiac IKs protein conformations and applied a combination of protein segmentation and energy linearization to study this relationship computationally. Simulations reproduced the effects of the beta-subunit (KCNE1) on the alpha-subunit (KCNQ1) dynamics and function, observed in experiments. Mechanistically, KCNE1 increased the probability of “visiting” conducting pore conformations on …

Examining Environmental Hazards In Rental Homes And Habitability Laws In Clark County, Nevada, Jorge Luis Bertran

UNLV Theses, Dissertations, Professional Papers, and Capstones

It is well established that home conditions are linked to the health outcomes of occupants. There are over 880,000 housing units in Clark County, Nevada; nearly half of those are renter-occupied units (ROUs). Currently, there is limited research on the characteristics of environmental hazards found in Clark County ROUs and the strength of habitability statutes created to protect tenants from substandard housing. Understanding how renters in Clark County are affected by environmental hazards in ROUs and the processes by which landlords and tenants resolve grievances related to those hazards would benefit public health. It would enhance the ability to quickly …