Life Sciences Commons^™

Digital Fragment Analysis Of Short Tandem Repeats By High‐Throughput Amplicon Sequencing, Brian J. Darby, Shay F. Erickson, Samuel D. Hervey, Susan N. Ellis-Felege

Biology Faculty Publications

High‐throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high‐throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, …

Competition Dynamics Within Communities Of Desert Wildlife At Water Sources, Lucas Keith Hall

Theses and Dissertations

Water is a vital resource for species inhabiting arid and semi-arid regions and can shape the biotic communities that we observe. Because water is considered a limiting resource for many species in desert environments, there is the potential for competitive interactions between species to occur at or around water sources. For this dissertation I tested hypotheses related to resource competition among different species of wildlife in the Great Basin and Mojave Deserts of western Utah. Chapter one evaluated the influence of feral horses (Equus caballus) on patterns of water use by communities of native birds and mammals. Chapter …

Molecular Studies Of South American Teiid Lizards (Teiidae: Squamata) From Deep Time To Shallow Divergences, Derek B. Tucker

Theses and Dissertations

I focus on phylogenetic relationships of teiid lizards beginning with generic and species relationship within the family, followed by a detailed biogeographical examination of the Caribbean genus Pholidoscelis, and end by studying species boundaries and phylogeographic patterns of the widespread Giant Ameiva Ameiva ameiva. Genomic data (488,656 bp of aligned nuclear DNA) recovered a well-supported phylogeny for Teiidae, showing monophyly for 18 genera including those recently described using morphology and smaller molecular datasets. All three methods of phylogenetic estimation (two species tree, one concatenation) recovered identical topologies except for some relationships within the subfamily Tupinambinae (i.e. position of …

Effectiveness Of The Toxicant Drc-1339 In Reducing Populations Of Common Ravens In Wyoming, Luke W. Peebles, Michael R. Conover

Wildland Resources Faculty Publications

Common raven (Corvus corax) populations have increased several-fold in the western United States during the past century; these birds cause problems when they kill new-borne lambs and calves and depredate nests of greater sage-grouse (Centrocercus urophasianus). The toxicant DRC-1339 is used by U.S. Department of Agriculture/Animal and Plant Health Inspection Service Wildlife Services to manage common raven populations and reduce the severity of these problems, but it is difficult to determine how many ravens are killed by an application because carcasses are rarely found. We examined the effectiveness of DRC-1339 applications for preventative control of ravens at 3 landfills and …

1862 December 15 - Houghton Annual Report For Year 1862 (Statistics For 1861), Surveyor General’S Report To Governor Of California

Surveyor General Reports

Annual reports of the Surveyor General to the Governor of California concerning the surveying of state lands, county boundaries, roads, maps, population, agriculture, crops and appropriations.

Evaluation Of The Estrogenic And Osmoregulatory Impacts Of Exposure To 4-Nonylphenol Pollution In The Estuarine Arrow Goby, Clevelandia Ios, Kaitlin Marie Johnson

Master's Theses

Recent evidence indicates that some of California’s coastal estuaries are contaminated with the chemical 4-nonylphenol (4-NP). Tissue burdens of 4-NP detected in the intertidal arrow goby (Clevelandia ios) in California are among the highest recorded worldwide, however, it remains unknown whether these fish are impacted by this 4-NP contamination. 4-NP is an established endocrine disrupting compound with estrogenic properties that can alter reproductive function. Furthermore, evidence that estrogens can modulate iono- and osmo-regulatory function in fishes implies that estuarine fishes exposed to 4-NP may also experience an impaired ability to maintain hydromineral balance. In Chapter 1 of this …

Orrm6 Is A Novel Organellar Rna Recognition Protein Involved In Plastid Rna Editing In Arabidopsis Thaliana, Justin B. Hackett

Masters Theses

RNA editing is a conserved mechanism of post-transcriptional modification in eukaryotes that changes specific nucleotides in RNA transcripts. In flowering plants, this is limited to cytidine to uridine deaminations. Plastid RNA editing events are critical for plastid development and the loss of editing can result in untranslated or non-functional proteins. There have been 40 RNA editing events discovered in the Arabidopsis thaliana plastid. Recently organellar RNA recognition motif (ORRM) proteins have been shown to broadly affect plastid RNA editing and interact with sequence specific trans-factor pentatricopeptide repeat proteins (PPR). ORRM proteins contain a canonical RNA recognition motif that has been …

Influence Of Release Timing On Survival And Movements Of Translocated Mule Deer (Odocoileus Hemionus) In Utah, David C. Smedley

Theses and Dissertations

Translocation of wildlife has become common practice for wildlife managers charged with management of animals on increasingly modified landscapes. Translocation can be used to reduce population density in the source area, supplement existing populations, reestablish extirpated populations, and establish new populations. Mule deer (Odocoileus hemionus) are a species of great interest to the public in western North America. Although translocations have been used to manage mule deer, very little has been done to document the outcomes of this management practice. The purpose of this research was to evaluate movement, site fidelity, space use, and survival of translocated mule …

Rnai Induced Knockdown Of A Cadherin-Like Protein (Ef531715) Does Not Affect Toxicity Of Cry34/35ab1 Or Cry3aa To Diabrotica Virgifera Virgifera Larvae (Coleoptera: Chrysomelidae), Sek Yee Tan, Murugesan Rangasamy, Haichuan Wang, Ana Maria Vélez, James Hasler, David Mccaskill, Tao Xu, Hong Chen, Jessica Jurzenski, Matthew Kelker, Xiaoping Xu, Kenneth E. Narva, Blair D. Siegfried

Department of Entomology: Faculty Publications

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is an important maize pest throughout most of the U.S. Corn Belt. Bacillus thuringiensis (Bt) insecticidal proteins including modified Cry3Aa and Cry34/35Ab1 have been expressed in transgenic maize to protect against WCR feeding damage. To date, there is limited information regarding the WCR midgut target sites for these proteins. In this study, we examined whether a cadherin-like gene from Diabrotica virgifera virgifera (DvvCad; Gen-Bank accession # EF531715) associated with WCR larval midgut tissue is necessary for Cry3Aa or Cry34/ 35Ab1 toxicity. Experiments were designed to examine the sensitivity of WCR to …

Proteomic Profiling Of Serum Derived Exosomes From Prostate Cancer Patients, David Turay

Loma Linda University Electronic Theses, Dissertations & Projects

Touted among the major achievements in the diagnosis and management of Prostate cancer (PCa) in the past few decades has been, the dramatic decline of men with advanced/metastatic PCa at diagnosis coupled with a significant improvement ( >90%) in the five and ten year survival rates of the disease. Non-palpable PCa (potentially clinically treatable disease) now accounts for 70-80% of all newly diagnosed cases of PCa. Preceding these changes by about a decade was the introduction of Prostatic Specific Antigen (PSA) into clinical practice; first as biomarker for monitoring response to therapy and subsequently as a complementary screening tool. It …

Genes Encoding Flower- And Root-Specific Functions Are More Resistant To Fractionation Than Globally Expressed Genes In Brassica Rapa, Naiyerah F. Kolkailah

Master's Theses

Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history. Brassica rapa is particularly valuable for studying genome evolution because it also experienced whole genome triplication shortly after it diverged from the common ancestor it shares with Arabidopsis thaliana about 17-20 million years ago. While many B. rapa genes appear resistant to paralog retention, close to 50% of B. rapa genes have retained multiple, paralogous loci for millions of years and appear to be multi-copy tolerant. Based on previous studies, gene function may contribute to the selective pressure driving certain genes back to singleton …

The Effects Of Quorum Sensing And Temperature On The Soluble Proteome Of Vibrio Salmonicida, Christopher L. Massey

Master's Theses

Vibrio salmonicida causes cold-water vibriosis in salmon populations around the world and causes financial damage to fisheries designed to farm these salmon. Very little is known about the physiology of how V. salmonicida causes disease and measures to contain vibriosis are restricted to either vaccinating individual fish against disease or administering antibiotics when an outbreak is detected. These procedures are costly and increase the risk for selection of antibiotic-resistant V. salmonicida strains. A recent reoccurrence of outbreaks in Norwegian fisheries provided incentive to better understand the virulence mechanisms of V. salmonicida. In this thesis, a proteomic approach was used to …

Rearing Temperature Affects The Expression Of Proteins In The Adhesive Of The Striped Acorn Barnacle, Balanus Amphitrite, Melissa J. Daugherty

Master's Theses

Barnacles are dominant hard–fouling organisms in marine waters. They attach to substrates by secreting a complex proteinaceous adhesive. Understanding the chemical composition of this multi–protein underwater adhesive and how it is affected by environmental variables, such as oceanic temperatures, is critical for developing nontoxic solutions to control biofouling. Previous experiments in our lab revealed an inverse relationship between critical removal stress (CRS) and temperatures at which barnacles were reared. Further investigations showed that this correlation is not attributed to differences in physical properties such as barnacle size or short–term changes in the viscosity of adhesive. Therefore, the observed effects may …

Comparison Of Foaming Properties Between Chelated Reconstituted Smp And Caseinates, Boya Liu

Master's Theses

Caseinate powders have been well accepted because of their foaming properties. In this study, 10% solution of reconstituted skim milk powder (SMP) chelated with sodium hexametaphosphate (SHMP) and trisodium citrate (TSC) at 1 mEq, 50 mEq, and 100 mEq were prepared to conduct a comparison with sodium caseinate, potassium caseinate, and calcium caseinate solutions. Foamability, foam stability as well as the preferential locations of αs-casein, β-casein and !-casein in their foams were analyzed. It was hypothesized that the foamability, foam stability and the preferential locations of these three caseins in the milk foams are different from treatment to treatment. Milk …

Glomus Tumor Of Trachea In An Adult Male, Sidra Arshad, Zubair Ahmad, Nasir Ud Din

Department of Pathology and Laboratory Medicine

Glomus tumors most commonly occur in distal extremities, particularly in the subungual region. The origin of these tumors is modified smooth muscle cells of glomus bodies. Trachea is one of the rare sites where normal glomus bodies may be sparse or absent, so occurrence of glomus tumor in trachea is very rare. Only 30 cases have been reported in the literature so far. In this case report, the authors describe a very rare and in fact first case of glomus tumor of trachea in a 45-year male Pakistani patient.

The Role Of The Transcriptional Antiterminator Rfah In Lipopolysaccharide Synthesis, Resistance To Antimicrobial Peptides, And Virulence Of Yersinia Pseudotuberculosis And Yersinia Pestis, Jared Michael Hoffman

Theses and Dissertations

RfaH is a unique bacterial protein that enhances transcription of a select group of long operons in many Gram-negative bacteria. Operons regulated by RfaH possess an upstream operon polarity suppressor sequence, which recruits the RfaH protein to the RNA polymerase during transcription of genes, most of which are involved in the synthesis of cell-surface features. These include synthesis of the lipopolysaccharide (LPS) core and O-antigen in Salmonella and Escherichia coli, as well as F-plasmid conjugation pilus and capsule in E. coli. LPS is an important virulence factor in many Gram-negative bacteria, and protects Y. pseudotuberculosis against host antimicrobial …

Association Between Expanded Normal Weight Obesity And Insulin Resistance Among U.S. Adults In The National Health And Nutrition Examination Survey, Keilah Elizabeth Martinez

Theses and Dissertations

The purpose of this investigation was to expand the evaluation of Normal Weight Obesity (NWO) and its association with insulin resistance using a nationally representative sample of U.S. adults. A cross-sectional study including 5,983 subjects was conducted. Body fat percentage was assessed using dual energy X-ray absorptiometry (DXA). Expanded Normal Weight Obesity (eNWO) categories (pairings of BMI and body fat percentage classifications) were determined by standard cut-points for BMI and the gender specific median for body fat percentage. Homeostatic Model Assessment-Insulin Resistance (HOMA-IR) levels were used to index insulin resistance. Mean ± SE values were as follows: BMI: 27.9 ± …

Review Of "The Least Likely Man: Marshall Nirenberg And The Discovery Of The Genetic Code" By F. H. Portugal, John B. Jenkins

Biology Faculty Works

No abstract provided.

Assessing Genetic Variation Of Rocky Mountain Bighorn Sheep At Elk Mountain, Brynn L. Parr, Rebeca L. Juarez, Jonathan A. Jenks

The Prairie Naturalist

The bighorn sheep (Ovis canadensis canadensis) herd occupying the Elk Mountain Region of South Dakota and Wyoming was established in 2001 with 20 individuals. An additional 7 ewes were released in 2004. The population increased to approximately 120 individuals in 2009, but subsequently declined to an estimated 80 individuals. Because of the low population size used to establish the herd and relative isolation of the Elk Mountain Region, potential factors associated with the population decline included reduced genetic diversity. Our objectives were to: 1) assess genetic diversity, 2) measure effective population size (Ne), and 3) compare the genetic diversity of …

Keys To Lichens Of North America, Revised And Expand- Ed. Irwin M. Brodo (Photographs By Sylvia Duran Sharnoff And Stephen Sharnoff; Drawings By Susan Laurie-Bourque)., Caleb A. Morse

The Prairie Naturalist

It would be hard to overestimate the importance of the 2001 publication of Lichens of North America (hereafter LNA) by Irwin Brodo, Silvia Duran Sharnoff, and Stephen Sharnoff (Brodo et al. 2001). Beautifully illustrated, LNA included both an excellent overview to lichenology—including such diverse topics as chemistry, ecology, ethnolichenology, and specimen preparation—and descriptions of more than 800 of the common and charismatic lichens of North Ameri- ca. It is the rare book that provides a good introduction to the discipline, while serving as an essential tool for lichenologists. LNA is frequently cited in journals as an authoritative source on spot …

Varmints And Victims: Predator Control In The Ameri- Can West. Frank Van Nuys., Phil Mastrangelo

The Prairie Naturalist

Having recently retired after 30+ years working in the field of human-wildlife conflicts, including predator conflicts with livestock, I looked forward to reading Varmints and Victims: Predator Control in the American West by Frank Van Nuys. As a wildlife biologist with an interest in the history of wildlife management in North America, I was further intrigued by the subject matter selected by Van Nuys.

In the book’s introduction, Van Nuys explains how the issue of mountain lion (Puma concolor) management in his home state of South Dakota sparked his interest in further exploring the history of predators and their management …

A Comparison Of Catabolic Pathways Induced In Primary Macrophages By Pristine Single Walled Carbon Nanotubes And Pristine Graphene, Caroline More, Jennifer Mcintyre, Luke O'Neill, Hugh Byrne

Articles

Understanding the correlation between the physico-chemical properties of carbonaceous nanomaterials and how these properties impact on cells and subcelluar mechanisms is critical to their risk assessment and safe translation into newly engineered devices. Here the toxicity, uptake and catabolic response of primary human macrophages to pristine graphene (PG) and pristine single walled carbon nanotubes (pSWCNT) are explored, compared and contrasted. The nanomaterial toxicity was assessed using three complementary techniques (live-dead assay, real time impedance technique and confocal microscopic analysis), all of which indicated no signs of acute cytotoxicity in response to PG or pSWCNT. Transmission electron microscopy (TEM) demonstrated that …

Effect Of Canopy Cover Of Capparis Decidua Forsk. On Soil Conditions In Thal Desert, Ghulam Yasin, Muhammad Farrakh Nawaz, Faiz Rasool, Muhammad Talha Bin Yousuf, Muhammad Qaisar Nazir, Atif Javed

Journal of Bioresource Management

Desert shrubs have a deep root system which allows them to explore the soil minerals and moisture from deeper horizons of soil and strongly support the local dwellers’ livelihoods. Capparis decidua (Forsk.) Edgew, generally known as karir, a xerophytic, densely branched shrub, is widely found in arid and semi-arid areas of Pakistan. The present study was conducted at four different sites in the Thal desert to determine the canopy effect of C. decidua on soil nutrients. Soil nutrients under the plant canopy (UC), at a distance of 150 cm away from the canopy (D150) and 300 cm away from the …

Microwave Assisted Extraction Of Phenolics From Trachyspermum Ammi (L.) Sprague, Sumera Javad, Maimoona Mubarik, Arusa Aftab, Amina Tariq

Journal of Bioresource Management

Trachyspermum ammi (L.) Sprague is an annual herbaceous plant belonging to the family Apiaceae and is mostly administered for stomach disorders. During the present research work, cold maceration and Microwave Assisted Extraction (MAE) of T. ammi Sprague was done by using methanol, dichloromethane and n-hexane separately as extracting solvents. For cold maceration, 2, 4, 6, 18 and 24 hours of time durations were used for each solvent. Maximum extract (50mg/g) was obtained at 18 hours of cold maceration with methanol, while maximum phenolics were also obtained from the same extract, which were calculated to be 170.89μg/g equivalent of Gallic acid. …

Evaluation Of Diver® Concentration Against Cotton Mealybug, Phenacoccus Solenopsis (Hemiptera: Pseudococcidae) And Its Parasitoid, Aenasius Bambawalei (Hymenoptera: Encyrtidae) In Laboratory, Muhammad Arfat Ashraf, Saif -Ur- Rehman, Nazeer Ahmed, Muhammad Salman Hameed, Saeed Ahmed, Zelle Huma

Journal of Bioresource Management

Bio-assay of Diver® for mealy-bug and its parasitoid, A. bambawalei, was carried out during 2010-2011 in the IPM Laboratory, Department of Agri. Entomology, University of Agriculture, Faisalabad. All the concentrations of Diver®, which were applied in laboratory conditions, were effective against mealy-bug. Diver® is the best mineral oil to control mealy-bug when compared to other synthetic pesticides. On the numerical basis of data, which were recorded on mortality basis, the highest concentration of Diver® was most effective against mealy-bug, followed by the other concentrations. All the concentrations of Diver® on the parasitoid of mealy-bug swerve less and their effects …

Impact Of Pre-Emergence Herbicides For The Control Of Weeds In Chick Pea (Cicer Arietinum L.) Under Hot Arid Climate, Ghulam Abbas, Aziz Ahmed, Marghub Amer, Zafar Abbas, Mudassir -Ur- Rehman, Aamir Hussain, Ghulam Abbas Khan

Journal of Bioresource Management

The experiments were conducted at Adaptive Research Farm Karor Lal Eason and farmers’ field, i.e. Mouza Nawan Kot, Tehsil Choubara during Rabi 2014-15. The purpose of the experiment was to evaluate the effect of different herbicides for the control of weeds on chick pea.Two pre-emergence herbicides with two different doses, viz. Pendimethalin330 EC @ 2500 ml ha-1 before sowing, Pendimethalin330 EC @ 3750 ml ha-1before sowing, Top Max 90% EC. (Metachlor 83% + Pendimethalin13%) @ 2250 ml ha-1 before sowing and TopMax 96% (Metachlor83% + 13%)@ 3350 ml ha-1, were tested. An untreated plot was also included in the experiment. …

Priming Cardiovascular Stem Cells For Transplantation Using Short-Term Hypoxia, Ivan Hernandez

Electronic Theses, Projects, and Dissertations

Conventional medical treatments fail to address the underlying problems associated with the damage inflicted by a coronary event. Thus, the long-term prognosis of patients admitted for heart failure is disheartening, with reported survival rates of 25 percent. Recent advances in stem cell research highlight the potential benefits of autologous stem cell transplantation for stimulating repair in heart tissue. However, a majority of those suffering from cardiovascular diseases are older adults whose autologous cells no longer possess optimum functional capacity. Additional work is needed to identify the optimal cell types or conditions that will promote cardiovascular regeneration across all age groups. …

Modification Of The In Vitro Uptake Mechanism And Anti-Oxidant Levels In Hacat Cells And Resultant Changes To Toxicity And Oxidative Stress Of G4 And G6 Poly (Amido Amine) Dendrimer Nanoparticles., Marcus Maher, Hugh Byrne

Articles

The mechanism of cellular uptake by endocytosis and subsequent oxidative stress has been identified as the paradigm for the toxic response of cationically surface charged nanoparticles. In an attempt to circumvent the process, the effect of increased cellular membrane permeability on the uptake mechanisms of poly (amidoamine) dendrimers generation 4 (G4) and 6 (G6) in vitro was investigated. Immortalised, non-cancerous human keratinocyte (HaCaT) cells were treated with DL-Buthionine-(S,R)-sulfoximine (BSO). Active uptake of the particles was monitored using fluorescence microscopy to identify and quantify endosomal activity and resultant oxidative stress, manifest as increased levels of reactive oxygen species, monitored using the …

Bathymetric Survey For Lakes Azuei And Enriquillo, Hispaniola, Michael Piasecki, Mahrokh Moknatian, Fred Moshary, Joseph Cleto, Yolanda Leon, Jorge Gonzalez, Daniel Comarazamy

Publications and Research

The two largest lakes on the Caribbean Island of Hispaniola, Lake Azuei in Haiti and Lake Enriquillo in the Dominican Republic, have experienced dramatic growth and surface area expansion over the past few years leading to severe flooding and loss of arable land around the lake perimeters. In order to better understand the reasons for this unprecedented rate of expansion and the resulting consequences a multi-disciplinary team comprised of researchers from Haiti, the DR, and the US have embarked on an extensive data collecting and hydrologic and climatological modeling campaign. While the sensor deployment entails stations that measure climatological data …

Canned Vegetable And Fruit Consumption Is Associated With Changes In Nutrient Intake And Higher Diet Quality In Children And Adults: National Health And Nutrition Examination Survey 2001-2010, Marjorie Freedman, Victor Fulgoni

Faculty Publications

Background Canned vegetables and fruit (CV+CF) are ubiquitous throughout the food supply. Yet information regarding their specific contribution to nutrient intake and health measures is lacking.Objective The objective of this study was to examine the association of CV+CF with nutrient intake, diet quality, anthropometric indicators of overweight/obesity, and blood pressure in a nationally representative population.Design and participants A secondary analysis of cross-sectional data from 17,344 children and 24,807 adults in the National Health and Nutrition Examination Survey 2001-2010 was conducted. A dataset was developed that distinguished CV+CF consumers from nonconsumers.Main outcome measures Diet quality was calculated using the Healthy Eating …