Life Sciences Commons^™

Shoreline Characterization In The Northern Indian River Lagoon, Melinda Donnelly, Michelle Shaffer, Suzanne Connor, Linda Walters

CEELAB Research Data

The purpose of this project was to evaluate current conditions of estuarine shorelines in the northern section of the Indian River Lagoon system, including Mosquito Lagoon, north Indian River, and Banana River. From January 2016 through June 2018, we evaluated structural and functional characteristics of 374 miles of shoreline, from Ponce Inlet in Volusia County to Sebastian Inlet in Brevard County (11,000+ data points). Hard-armoring accounted for approximately 50% of total shoreline, evenly divided between shoreline with bulkheads (25%) and hardened slopes (25%). Forty-five percent of shoreline without hard-armoring had anthropogenic alterations (i.e. mosquito impoundments, railroads and roadways, residential and …

Usu Careers In Agriculture, Forestry, Natural Resources, Grades 9-12, Tyson Sorensen, Olivia Horning, Joshua Dallin

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These are brochures (three currently have been completed) that were developed as part of this grant to promote AFNR careers among high school-aged students. These brochures were developed with a focus on careers related to Genetic Engineering and Biotechnology. The brochures were distributed to participants of the workshop and with invitations for them to also distribute the brochures to their school's career/guidance counselors. The goal of the brochures is to help students learn about and see the pathway to get to their agriculture, forestry, or natural resources career of interest.

Brochure titles:

Animal, Dairy and Veterinary Sciences (BS): Biotechnology Emphasis …

Mitochondrial Dna Sequence Alignments For Phylogenetic Analysis Of The Shrimp Genus Farfantepenaeus, Laura Timm, S. Simon, Heather Bracken-Grissom Dr.

DEEPEND Datasets

This dataset includes 12S, 16S, and COI sequence data. Sequences were obtained from the eight recognized species of Farfantepenaeus: F. aztecus, F. brasiliensis, F. brevirostris, F. californiensis, F. duorarum, F. isabelae, F. notialis, and F. subtilis. Also included are several sequences from species of Litopenaeus, which serve as outgroup(s).

Gulf-Wide Seafloor Surface Benthic Foraminifera Stable Isotopes From Sediment Cores Collected On Multiple Cruises From 2010-06-13 To 2017-07-19, Patrick Schwing, David J. Hollander

C-IMAGE data

This dataset includes baseline stable carbon and oxygen isotope measurements from benthic foraminifera throughout the Gulf of Mexico. Stable isotope measurements were performed on Cibicidoides spp. The dataset contains the sediment core information such as location, date, and depth; and benthic foraminiferal stable carbon and oxygen isotopes. Sediment cores were collected on multiple cruises from 2010-06-13 to 2017-07-19.

Benthic Foraminiferal Assemblages From Sediment Cores Collected On Multiple Cruises In The Gulf Of Mexico From 2010-11-18 To 2017-05-22, Patrick Schwing, David J. Hollander

C-IMAGE data

This dataset includes baseline assemblage measurements from benthic foraminifera throughout the Gulf of Mexico. The dataset is a compilation of seafloor surface benthic foraminifera assemblages from sediment cores collected on multiple cruises and field sampling in the Gulf of Mexico from 2010-11-18 to 2017-05-22. The dataset contains the Gulf-wide diversity indices and the full benthic taxonomic counts for two regions: Cuba and the southern Gulf of Mexico. The Gulf-wide file contains the total density and diversity calculations using Fisher’s Alpha and Shannon indices from the surface-most sub-sample from each core (typically 0-2 mm). The Gulf-wide spreadsheet is comprised of data …

A Climatological Dataset Of Nutrient, Chlorophyll, And Particulate Matter Distributions On The Ross Sea Continental Shelf Derived From Cruise-Based Measurements Spanning 1967 To 2016, Walker O. Smith Jr., Daniel E. Kaufman

Data

This dataset includes data used in the publication Smith and Kaufman (2018), Progress in Oceanography, which examines the temporal and spatial distributions of nutrients and particulate matter in the Ross Sea continental Shelf using cruise-based observations, and compares the resulting annual productivity estimates with previously reported satellite-based estimates. Specifically, these data represent distributions of nutrients, chlorophyll, particulate organic carbon, particulate organic nitrogen, and biogenic silica that were compiled from 42 cruises (from 1967 - 2016) to the Ross Sea continental shelf to generate a comprehensive climatological dataset for November, December, January, and February. This climatology provides a novel look at …

Red Fox Genome Assembly Identifies Genomic Regions Associated With Tame And Aggressive Behaviours, Anna V. Kukekova, Jennifer L. Johnson, Xueyan Xiang, Shaohong Feng, Shiping Liu, Halie M. Rando, Anastasiya V. Kharlamova, Yury Herbeck, Natalya A. Serdyukova, Zijun Xiong, Violetta Beklemischeva, Klaus Peter Koepfli, Rimma G. Gulevich, Anastasiya V. Vladimirova, Jessica P. Hekman, Polina L. Perelman, Aleksander S. Graphodatsky, Stephen J. O’Brien, Xu Wang, Andrew G. Clark, Gregory M. Acland, Lyudmila N. Trut, Guojie Zhang

Biology Faculty Articles

Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes …

Bee Attractiveness Data, Bernadette Maria Mach, Daniel A. Potter

Entomology Research Data

Urban and suburban landscapes can be refuges for biodiversity of bees and other pollinators. Public awareness of declining pollinator populations has increased interest in growing plants that provide floral resources for bees. Various publications and websites list “bee-friendly” plants, but such lists are rarely based on empirical data, nor do they emphasize flowering trees and shrubs, which are a major component of urban landscapes. We quantified bee visitation to 72 species of flowering woody landscape plants across 373 urban and suburban sites in Kentucky and southern Ohio, USA, sampling and identifying the bee assemblages associated with 45 of the most …

Bee Assemblages Data, Bernadette Maria Mach, Daniel A. Potter

Entomology Research Data

Urban and suburban landscapes can be refuges for biodiversity of bees and other pollinators. Public awareness of declining pollinator populations has increased interest in growing plants that provide floral resources for bees. Various publications and websites list “bee-friendly” plants, but such lists are rarely based on empirical data, nor do they emphasize flowering trees and shrubs, which are a major component of urban landscapes. We quantified bee visitation to 72 species of flowering woody landscape plants across 373 urban and suburban sites in Kentucky and southern Ohio, USA, sampling and identifying the bee assemblages associated with 45 of the most …

Medline-Indexed, In Process For Medline, And Non-Indexed Records Added To Pubmed And Pubmed Central, 1990 And 2000-2017, Peace Ossom-Williamson, Christian I.J. Minter

UTA Libraries Datasets

These files include the underlying data from the PubMed and Scholarly Communication research investigation.

Presence/Absence And Density Data For Epipelagic Tows Collected During R/V Blazing Seven Cruises Lf2016a And Lf2016b, Northern Gulf Of Mexico From 2016-06-09 To 2016-07-28, Jay R. Rooker, David Wells

DEEPEND Datasets

This dataset reports presence/absence and density data for epipelagic tows collected in the northern Gulf of Mexico during R/V Blazing Seven cruises LF2016A and LF2016B (2016-06-09 to 2016-07-28). Larval fishes were sampled from 48 stations and cruise data were collected at each site including latitude/longitude, date, time, environmental data (temperature, salinity, dissolved oxygen) and Sargassum dry weight. Larval catch data before and after the oil spill will be compared to improve our understanding of the causes of temporal variability as it relates to the Deep-Water Horizon oil spill (DWHOS). Habitat associations of selected taxa (billfishes, tunas, dolphinfishes, flyingfishes) will be …

Catch Data From Fish Collected Throughout The Gulf Of Mexico From 2011 Until 2017, Steven A. Murawski

C-IMAGE data

This dataset represents collections taken by demersal longline fishing gears throughout the Gulf of Mexico from 2011 until 2017. They include station location information and standardized fish catch data (numbers, weights, sex, length). Catch data were classified into five sub-regions: West Florida Shelf (WFS), North Central (NC), North West (NW), South West (SW), Yucatan Peninsula (YP) and Cuba (CUB). Catch data were also classified into four species groups: Elasmobranch (EL), Other demersal (OD), Pelagic (LP) and Snapper/Grouper (SG). Data from 2011 until 2014 are also reported in C-IMAGE I dataset R1.x135.120:0002, Lesion data from fish collected off Terrebonne Bay, LA …

Inventory Of Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruise Dp05) In The Gulf Of Mexico From 2017-05-01 To 2017-05-11, April Cook, Tracey Sutton

DEEPEND Datasets

This dataset includes an inventory of Gulf of Mexico oceanic fauna data including species, weight, and measurements collected from R/V Point Sur (Cruise DP05) from 2017-05-01 to 2017-05-11. The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled …

Microtubule Seams Are Not Mechanically Weak Defects, Taviare Hawkins

Physics Faculty Scholarship

Microtubule rigidity is important for many cellular functions to support extended structures and rearrange materials within the cell. The arrangement of the tubulin dimers within the microtubule can be altered to affect the protofilament number and the lattice type. Prior electron microscopy measurements have shown that when polymerized in the presence of a high concentration of NaCl, microtubules were more likely to be ten protofilaments with altered intertubulin lattice types. Specifically, such high-salt microtubules have a higher percentage of seam defects. Such seams have long been speculated to be a mechanically weak location in the microtubule lattice, yet no experimental …

The Complete Phylogeny Of Pangolins: Scaling Up Resources For The Molecular Tracing Of The Most Trafficked Mammals On Earth, Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T. Stanley, Stephen J. O'Brien, Warren E. Johnson, Shu Jin Luo

Biology Faculty Articles

Pangolins, considered the most-traffcked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here, we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and 9 nuclear genes. We confrm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca. 23 million years ago (Ma) (95% HPD = 18.7-27.2), limited fossil evidence suggesting dispersals from Europe. We recognize 3 genera including Manis (Asian pangolins), Smutsia (large African pangolins), and Phataginus …

A Time Course Study Of Rotavirus-Infected Intestinal Cells Treated With Stilbenoids And The Regulation Of Apoptosis, Rebecca D. Parr, Caleb M. Witcher, Rebekah Napier-Jameson, Hannah L. Wilson, Stormey Wisdom, Macie N. Mattila, Essence B. Strange, Josephine Taylor, Beatrice Clack, Fabricio Medina-Bolivar, Judith M. Ball

Faculty Publications

This is a time course study of virus –host interactions that are modified with the addition of two small natural products. They appear to effect virus replication and the host response to the infection.

Impact Of Basal Diet On Obesity Phenotype Of Recipient Mice Following Fecal Microbiome Transfer From Obese Or Lean Human Donors. Appendix D. Microbiome Sequencing Data, Daphne Rodriguez, Abby D. Benninghoff, Korry Hintze

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The complete data set generated by 16S rRNA sequencing of all fecal samples analyzed is provided as a digital data .biom file accessible.

Input, Output And Complete Run Files For The Atlantis Ecosystem Model Deepwater Horizon Oil Spill Simulations, Cameron Ainsworth

C-IMAGE data

Data are complete input, output, and executable model run files for Atlantis simulations of the Deepwater Horizon oil spill. The model outputs in these folders describe simulations from 2010 to 2035; the spatial domain is the entire Gulf of Mexico. Simulations are published as Ainsworth, C.H., Paris, C.B., Perlin, N., Dornberger, L.N., Patterson, W., Chancellor, E., Murawski, S., Hollander, D., Daly, K., Romero, I.C., Coleman, F. and Perryman, H. 2018. Impacts of the Deepwater Horizon oil spill evaluated using an end-to-end ecosystem model. PLoS One, 13(1): e0190840 doi: 10.1371/journal.pone.0190840

Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng

Biology Faculty Articles

Hepatocellular carcinoma (HCC) is the most frequent malignancy of the liver. Transforming growth factor beta 1 (TGFB1) and marker of proliferation Ki-67 (MKI67) regulate cell proliferation, differentiation, and growth. The association between MKI67 and TGFB1 expression and its clinical implications in HCC remain unknown. Methods: Public databases were used to analyze TGFB1 and MKI67 expression in different pathologic grades/stages and tissue types of HCC. The association between MKI67 and TGFB1 expression was explored using pathway analysis and in a HepG2 cell line treated with TGFB1. Survival analysis was performed to evaluate the prognostic value of TGFB1 and MKI67 expression in …

Data Files Column Key: Effects Of Amur Honeysuckle (Lonicera Maackii) On Headwater Streams, Julia I. Chapman, Eric B. Borth, Ryan W. Mcewan

Data Files

Document provides a description for each column heading used in the data files contained in the collection "Effects of Amur Honeysuckle (Lonicera maackii) on Headwater Streams."

File is in comma-separated values (.csv) format; to view the file in Excel (.xlsx), see the supplemental file.

Ichthyology Field Notebooks Spreadsheet, Karisa Boyer

Ichthyology Collection

No abstract provided.

Salvinia Radseq, Carol A. Rowe, Donald Hauber, Paul G. Wolf

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No abstract provided.

Reproductive Success Of Mountain Pine Beetle Infesting Cut Bolts Of Great Basin Bristlecone Pine, Limber Pine, And Lodgepole Pine, Barbara J. Bentz, Karen E. Mock, Erika L. Eidson

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The preference-performance hypothesis states that ovipositing phytophagous insects will select host plants that are well-suited for their offspring and avoid host plants that do not support offspring performance (survival, development and fitness). The mountain pine beetle (Dendroctonus ponderosae), a native insect herbivore in western North America, can successfully attack and reproduce in most species of Pinus throughout its native range. However, mountain pine beetles avoid attacking Great Basin bristlecone pine (Pinus longaeva), despite recent climate-driven increases in mountain pine beetle populations at the high elevations where Great Basin bristlecone pine grows. Low preference for a potential host plant species may …

Dataset For: Tracking An Oil Tanker Collision And Spilled Oils In The East China Sea Using Multisensor Day And Night Satellite Imagery, Shaojie Sun

C-IMAGE data

In this dataset, we used a multi-sensor day and night satellite approach to track the SANCHI oil tanker collision and oil spill event in January 2018 in the East China Sea. The drifted on fire oil tanker was tracked by Visible Infrared Imaging Radiometer Suite (VIIRS) Nightfire product and Day/Night Band (DNB) imagery. Such pathway and locations were also reproduced with a numerical model, with RMS error of < 15 km. MultiSpectral Instrument (MSI) optical imagery during daytime shows smokes on 13 January 2018, further confirms the drifted tanker location. MSI imagery after 4 days of the tanker’s sinking (18 January 2018) reveals oil on the ocean surface to the east and northeast of the tanker sinking location. This combination of all available remote sensing and modeling techniques can provide effective means to monitor marine accidents and oil spills to assist event response.

Dispersant Enhances Hydrocarbon Degradation And Alters The Structure Of Metabolically Active Microbial Communities In Shallow Seawater From The Northeastern Gulf Of Mexico, Lena Chu, Elisa Mercando, Roger C. Prince, Isabel C. Romero, David Hollander

C-IMAGE data

The seawater samples were collected from Pensacola Beach, FL in June and August, 2016. The seawater was incubated with low concentration of oil (2ppm) with or without dispersant. Oil analysis and sequencing data were generated.

Genetic Differentiation Between Two Species Of Buckwheat (Eriogonum), Paul G. Wolf, Jenessa B. Lemon

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Discovering the extent of genetic differentiation between closely related taxa facilitates decisions regarding species protection under the Endangered Species Act. Here, we analyze genotype data to explore the relatedness of two buckwheat species: Eriogonum soredium Reveal- a narrow endemic under consideration for protection, and a widespread close relative, Eriogonum shockleyi S. Watson. Eriogonum soredium grows only on Ordovician limestone outcroppings in west central Utah, whereas the range of E. shockleyi is broad, spanning the western United States from Colorado to California, and Idaho to Arizona. Eriogonum shockleyi is suspected of hybridizing with other buckwheats throughout this range. We detected higher …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

Whole-Genome Analysis Of Mycobacterium Tuberculosis From Patients With Tuberculous Spondylitis, Russia, Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Andrey Yurchenko, Anna Vyazovaya, Igor Mokrousov, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O’Brien

Biology Faculty Articles

Whole-genome analysis of Mycobacterium tuberculosis isolates collected in Russia (N = 71) from patients with tuberculous spondylitis supports a detailed characterization of pathogen strain distributions and drug resistance phenotype, plus distinguished occurrence and association of known resistance mutations. We identify known and novel genome determinants related to bacterial virulence, patho-genicity, and drug resistance.

Evaluation Of Diet Matrix Uncertainty For The Atlantis Model, Cameron Ainsworth

C-IMAGE data

We conducted 1000 Atlantis simulations, using permutated diet matrices created by drawing from a beta distribution that represented uncertainty in predator diet. We also employed a statistical emulator which simulates the production of many more Atlantis runs than could be achieved through numerical simulation. This dataset includes 3 products: statistical emulator output, diet matrices, and Atlantis simulations. These are each contained in their own zip file.

Allenrolfea Wetland Genetics Data, Paul G. Wolf, Carol A. Rowe, Robert W. Lichvar

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The hydrophyte Allenrolfea occidentalis (S. Watson) Kuntze (iodine bush) is a halophytic shrub of the arid southwest that is listed as a facultative wetland (FACW) species on the National Wetland Plant List. This rating means the species is usually a hydrophyte but occasionally is found in uplands. We tested for genetic (ecotypic) differences between plants sampled from wetlands versus uplands. We used genotyping-by-sequencing (ddRAD-seq) to generate data from 133 plants from 30 locations representing both wetland and upland occurrences for over 1300 loci. Analyses indicated that the strongest signal is differences in geographic distribution: samples that are in close geographic …