Research Methods in Life Sciences Commons^™

Effectiveness Of Different Agricultural Management Styles As Insect Biological Corridors: A Comparison Of Insect Populations In Fragmented Chocó Cloud Forest, Ecuador, Tara M. Krantz

Independent Study Project (ISP) Collection

Insects are part of the most diverse class of animals on the planet and are essential to various ecological functions such as pollination, nutrient cycling, providing a food source for other taxa, and more. The diversity and ecological services of insects are necessary to the operation of agriculture because of pest control and pollination of crops. However, the diversity of insects is severely reduced due to fragmentation. It is currently not well understood if certain types of agriculture can lessen the impact of fragmentation on natural and crop-based insect communities. In this study, insect populations in four different agricultural management …

Cambios En El Cronograma De Temporadas Reproductivas De Pingüinos De Magallanes (Spheniscus Magellanicus): Relaciones Entre Eventos Fenológicos Y Variables Climáticas, Grace Neumiller

Independent Study Project (ISP) Collection

Estudios a largo plazo han demostrado que hay fluctuaciones a lo largo de la fenología de la vida silvestre a causa de los cambios climáticos (Black, 2016). Los pingüinos de Magallanes (Spheniscus magellanicus) exhiben cambios en el cronograma de los eventos fenológicos de sus temporadas reproductivas a causa de variables oceanográficas y climáticas de su ambiente. A partir de fotos de cámaras trampas, este trabajo describe y analice algunos eventos en la fenología de los pingüinos de Magallanes en Isla Martillo, Canal Beagle, Tierra del Fuego, Argentina: el inicio de la temporada reproductiva, el periodo de muda de pichones, y …

Araneae Biodiversity In The Amazonian Foothills: An Analysis Of Family And Guild Presence Across Habitat Types, Rae Lewark

Independent Study Project (ISP) Collection

The activity of the order Araneae within ecosystems is often considered an ecological mystery. Considered top-level trophic predators, spiders act as regulators of insect populations and have influence upon the foundation of the trophic web. In the Ecuadorian Amazonian foothills, it is important to address the lack of knowledge of the biodiversity of spiders in the region. Conducting biodiversity studies across land use gradients can begin to characterize anthropogenic impacts on neotropical spider species. This study quantifies the araneae biodiversity in the transition between the Cloud and Amazon forests in Ecuador. Populations in primary forest, secondary forest, cultivated fields and …

An Animal-Assisted Intervention Study In The Nursing Home: Lessons Learned, Lonneke G. J. A. Schuurmans, Inge Noback, Jos M. G. A. Schols, Marie-Jose Enders-Slegers

People and Animals: The International Journal of Research and Practice

AAI studies in the nursing home pose a specific set of challenges. In this article the practical and ethical issues encountered during a Dutch psychogeriatric nursing home AAI study are addressed with the aim of sharing our experiences for future researchers as well as AAI practitioners in general.

In our study we compared three groups of clients with dementia who participated in group sessions of either visiting dog teams, visiting FurReal Friend robot animals, or visiting students (control group) and monitored the effect on social interaction and neuropsychiatric symptoms through video analysis and questionnaires. We encountered the following four categories …

Animal Research, Accountability, Openness And Public Engagement: Report From An International Expert Forum, Elisabeth H. Ormandy, Daniel M. Weary, Katarina Cvek, Mark Fisher, Kathrin Herrmann, Pru Hobson-West, Michael Mcdonald, William Milsom, Margaret Rose, Andrew Rowan, Joanne Zurlo, Marina A.G. Von Keyserlingk

Oversight of Animal Experimentation Collection

In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to …

Rcrab: An R Analytics Tool To Visualize And Analyze The Movement Of Horseshoe Crabs In Long Island Sound, Ismael Youssef, Samah Senbel, Jo-Marie Kasinak, Jennifer Mattei

School of Computer Science & Engineering Faculty Publications

Mark-recapture programs are important for studying the ecology and population dynamics of wildlife. An R shiny analytics tool was developed to track the movement of horseshoe crabs in Long Island Sound based on tag and resight data. The crabs were tagged and recaptured by volunteers of Project Limulus, a community-based research program. The dataset contains tag and recapture location information for 14,065 horseshoe crabs over 18 years. The dataset was initially cleaned by removing records with missing, duplicate or incorrect data. A new data structure was developed to save the data and simplify processing: Three dimensions were used, one for …

Automated Monitoring Of Behaviour In Zebrafish After Invasive Procedures, Anthony G. Deakin, Jonathan Buckley, Hamzah S. Alzu'bi, Andrew R. Cossins, Joseph W. Spencer, Waleed Al'nuaimy, Iain S. Young, Jack S. Thomson, Lynne U. Sneddon

Validation of Animal Experimentation Collection

Fish are used in a variety of experimental contexts often in high numbers. To maintain their welfare and ensure valid results during invasive procedures it is vital that we can detect subtle changes in behaviour that may allow us to intervene to provide pain-relief. Therefore, an automated method, the Fish Behaviour Index (FBI), was devised and used for testing the impact of laboratory procedures and efficacy of analgesic drugs in the model species, the zebrafish. Cameras with tracking software were used to visually track and quantify female zebrafish behaviour in real time after a number of laboratory procedures including fin …

Decrypting Female Attractivity In Garter Snakes, Holly Rucker

Senior Honors Projects, 2010-2019

Pheromones are utilized by many species as sexual signals driving mate choice, and pheromone production in vertebrates hinges on sex hormone action. Female red-sided garter snakes (Thamnophis sirtalis parietalis) produce a skin-based sex pheromone used by males for mate detection and selection. Estradiol is necessary for pheromone production, yet the specific mechanisms within the skin are unknown. Central to this is the metabolism of testosterone to estradiol via the enzyme aromatase. It is hypothesized that female garter snakes synthesize estradiol locally in the skin and maintain pheromone production via tissue-specific regulation of aromatase. Further, I hypothesize that female …

Is Animal-Based Biomedical Research Being Used In Its Original Context?, Constança Carvalho, Daniel Alves, Andrew Knight, Luís Vicente

Validation of Animal Experimentation Collection

No abstract provided.

Critically Evaluating Animal Research, Andrew Knight

Validation of Animal Experimentation Collection

No abstract provided.

Mammals Of The Northern Andes: An Analysis Of Camera Trap Data And Observation In Angochagua, Ecuador, Risa Berman

Independent Study Project (ISP) Collection

The high Andes of Ecuador are home to a diverse community of mammals, many of which are threatened. These include the Andean bear, Andean fox, puma, and mountain tapir. This study used camera traps, direct observation, and indirect observation over three weeks to monitor the wildlife in the mountains of the Parroquia of Angochagua. The five species observed during this period were Andean bear, Andean fox, dog, mountain paca, and mouse. While this short study did not completely survey the mammalian community of the area, it confirmed the presence, diet, sociality, temporal habits, elevational range, and habitat preferences of the …

Recent Efforts To Elucidate The Scientific Validity Of Animal-Based Drug Tests By The Pharmaceutical Industry, Pro-Testing Lobby Groups, And Animal Welfare Organisations, Jarrod Bailey

Validation of Animal Experimentation Collection

Background: Even after several decades of human drug development, there remains an absence of published, substantial, comprehensive data to validate the use of animals in preclinical drug testing, and to point to their predictive nature with regard to human safety/toxicity and efficacy. Two recent papers, authored by pharmaceutical industry scientists, added to the few substantive publications that exist. In this brief article, we discuss both these papers, as well as our own series of three papers on the subject, and also various views and criticisms of lobby groups that advocate the animal testing of new drugs.

Main text: We argue …

Spatial And Temporal Variability In Post-Larval Yellow Perch Density, Steve Hauschildt

Biology Graduate Theses

Yellow Perch Perca flavescens are important as forage for other species and for sport fishing in many northern lakes. However, estimating post-larval Yellow Perch populations can be difficult because of many environmental factors that cause unexplained variation. The objective of this study was to help reduce unexplained variation by determining a post-larval Yellow Perch population density estimate on Blackduck Lake, MN, provide guidance to help determine the number of trawls required for trawling-based recruitment indices to achieve varying levels of precision, and test for the effects of wind speed and direction on post-larval Yellow Perch spatial variability. This study estimated …

A Prairie And Its People: Conflict And Cooperation. E. Frank Schramm, Joseph E.A. Alexis, The Amos Eager Family, The University Of Nebraska And Other Notable Owners Of Nine Mile Prairie And Its Environs, Jon H. Oberg

University of Nebraska State Museum: Staff and Affiliates, Publications

This study looks at the social history of individuals connected to a particular geographic quadrant -- Section 1 of Middle Creek precinct, Lancaster County, Nebraska. This an area famous for its natural history, as it is the home of Nine Mile Prairie. But the property owners in this section have a colorful history that encompasses the fields of sports, politics, academics, foreign wars, and crime. The study looks primarily at E. Frank Schramm, Joseph E.A. Alexis, and the Amos Eager family, who with other owners contributed importantly to the history and development of the City of Lincoln and the State …

Extrapolation Of Animal Research Data To Humans: An Analysis Of The Evidence, Rebecca Ram

Validation of Animal Experimentation Collection

The ethical arguments against animal experimentation remain ever-strong. In addition, the scientific case against the use of animals in research grows more compelling, with exponential progress in the development of alternative methods and new research technologies. The Dutch authorities recently announced an ambitious, but welcome, proposal to phase out “the use of laboratory animals in regulatory safety testing of chemicals, food ingredients, pesticides and (veterinary) medicines” by 2025, as well as “the use of laboratory animals for the release of biological products, such as vaccines” (Netherlands National Committee for the protection of animals used for scientific purposes, NCad, 2016, p. …

Methods For Estimating Mountain Goat Occupancy And Abundance, Molly Mcdevitt

Graduate Student Theses, Dissertations, & Professional Papers

Abundance and occupancy are two parameters of central interest to the field of ecology. Furthermore, accurate (both precise and unbiased) estimates are key pieces to the puzzle of effective wildlife management decision-making. While there exist a variety of sampling techniques and statistical models for effectively estimating population parameters for frequently encountered and large mammals, methods for sampling unmarked and rare species are few and far between. The first step to acquiring usable parameter estimates is through the use of sampling theory and incorporation of probabilistic sampling designs to collect count-data and occurrence-data. Often, it is assumed that probabilistic sampling designs …

Population Health Of Spotted Salamanders (Ambystoma Maculatum) In Created Vernal Pools: An Integrative Approach, Alice R. Millikin

Graduate Theses, Dissertations, and Problem Reports (ETD)

Habitat creation is an important tool for conservation to counteract habitat loss and degradation. Vernal pools are susceptible to destruction due to limited detection, protection, and regulation. These wetlands provide fishless breeding habitat for many amphibian species including spotted salamanders (Ambystoma maculatum) in eastern North America. Determining whether created vernal pool habitat is successful is often determined by demographic data of colonizing populations. I suggest that hormone levels, population genetics, and disease prevalence can improve our understanding of population health in created habitat. The goal of this dissertation was to assess the health of spotted salamander larvae in …

Growth Of Pelagic Age-0 Yellow Perch In Relation To Hatch Dates And Water Temperature In North-Central Minnesota Lakes, Ethan Karppinen

Biology Graduate Theses

Exposure to consistent water warming rates and access to abundant populations of edible sized zooplankton affects growth and increases the probability of survival for newly hatched Yellow Perch Perca flavescens. Seven lakes with varying physical characteristics were selected in north-central Minnesota to study abiotic (water temperature) and biotic (zooplankton community and fish growth) progressions during the spring and early summer (April-June). Mean water temperatures from ice-out to 28 June (11.98-14.62 °C) had significant relationships with mean depth (P < 0.01, R? = 0.85), max depth (P < 0.01, R? = 0.73), and total volume (P < 0.01, R2 = 0.54). Hatch periods ranged from 13 to 19 days in 2015 and 13 to 25 days in 2016. Cumulative degree-days (CDD) were used to predict Yellow Perch hatch periods and explain growth. CDD predicted 21-81% of hatch periods in 2015 and 11-50% in 2016. Mean predicted total lengths at 28 June were 19.65-30.41 mm in 2015 and 20.88-28.54 mm in 2016. There was a significant relationship between CDD and predicted total length (R? = 0.62, P < 0.01) to explain differences in Yellow Perch total length while inhabiting the pelagic zone. Observed gape measurements were highly correlated with predicted gapes from the Schael formula (R? = 0.89, P < 0.01) that was used to assess the availability of edible sized zooplankton for age-0 Yellow Perch in each lake. No predator-prey mismatches were found and earlier hatch dates produced age-0 Yellow Perch with greater predicted total lengths in late June on the majority of lakes. This suggests that earlier hatched Yellow perch have an advantage over later hatched Yellow Perch in attaining greater lengths by late June. Our study provides information on a variety of physical and biological progressions in lakes, which may be used for fisheries management practices in the future.

Investigations Of Biotremors In The Veiled Chameleon (Chamaeleo Calyptratus), Kathryn C. Laslie

Masters Theses & Specialist Projects

While substrate-borne vibrations are utilized by different reptile species, true conspecific communication via biotremors has not yet been demonstrated in reptiles. This study follows a preliminary report that the veiled chameleon (Chamaeleo calyptratus) could produce biotremors in communicative contexts. I tested chameleon behavioral sensitivity to vibrations by placing them on a dowel attached to a shaker emitting vibrations of 25, 50, 150, 300, and 600 Hz and then measured their changes in velocity before and after the stimulus. I then paired chameleons in various social contexts [anthropogenic disturbance (human disruption of animal); dominance (malemale; female-female C. calyptratus); courtship (male-female C. …

Bird Abundance At Bird Feeders In Response To Temperature, Wind Speed And Precipitation During The Winter Season, Siddhant Kahal

Master's Theses

The goal of this project is to explore how 23 different bird species respond to 3 climatic attributes. These attributes are lower than average temperatures, wind speed and precipitation level. Information about the bird species and all of the data associated with them is provided by Project FeederWatch (PFW). This is a citizen based survey study that provides key information about bird species abundance through the use of backyard and community feeders. The study volunteers from across the United States and Canada monitor these bird feeders and note important information about the species such as the number of individuals seen. …

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

School of Computing: Faculty Publications

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to …

Population Characteristics Of A Closed Northern Pike (Esox Lucius) Catch-And-Release Population In Minnesota, John Kempe

Biology Graduate Theses

Literature regarding catch-and-release populations of Northern Pike are rare and provide a unique perspective on their population dynamics. Shingobee Lake is a 64- ha mesotrophic lake with a maximum depth of 12.2 m located in northern Minnesota. Northern Pike fishing has been catch-and-release only since 2005, and there are no public accesses on the lake. Annual ice-out trap-netting occurred from 2009-2017, and a sizable amount of the Northern Pike recaptured via trapnet or angling had been previously tagged (37-59%). The lack of exploitation and high tagging percentage provided a unique opportunity to study the population dynamics of Northern Pike. Shinogbee’s …

Estimating Exploitation Rates In The Alabama Red Snapper Fishery Using A High-Reward Tag–Recapture Approach, Dana K. Sackett, Mattgew Catalano, J. Marcus Drymon, Sean P. Powers, Mark Albins

University Faculty and Staff Publications

Accurate estimates of exploitation are essential to managing an exploited fishery. However, these estimates are often dependent on the area and vulnerable sizes of fish considered in a study. High-reward tagging studies offer a simple and direct approach to estimating exploitation rates at these various scales and in examining how model parameters impact exploitation rate estimates. These methods can ultimately provide a better understanding of the spatial dynamics of exploitation at smaller local and regional scales within a fishery—a measure often needed for more site-attached species, such as the Red Snapper Lutjanus campechanus. We used this approach to tag 724 …

Compression And Relaxation Of Fishing Effort In Response To Changes In Length Of Fishing Season For Red Snapper (Lutjanus Campechanus) In The Northern Gulf Of Mexico, Sean P. Powers, Kevin Anson

University Faculty and Staff Publications

A standard method used by fisheries managers to decrease catch and effort is to shorten the length of a fishery; however, data on recreational angler response to this simple approach are surprisingly lacking. We assessed the effect of variable season length on daily fishing effort, measured by using numbers of boat launches per day, anglers per boat, and anglers per day from video observations, in the recreational sector of the federal fishery for red snapper (Lutjanus campechanus) in coastal Alabama. From 2012 through 2017, season length fluctuated from 3 to 40 d. Daily effort, measured by using mean number of …

Does The Stress Inherent To Laboratory Life And Experimentation On Animals Adversely Affect Research Data?, Jarrod Bailey

Validation of Animal Experimentation Collection

Stress and distress in laboratory animals is often inherent and unavoidable. The effect of these factors on the reliability and relevance of experimental data is not sufficiently appreciated. Greater awareness, debate and discussion of this issue are urgently required.

“Everyday” Knowledge And A New Paradigm Of Animal Research, David Fraser, Jeffrey M. Spooner, Catherine A. Schuppli

Validation of Animal Experimentation Collection

Commentary on Marino and Allen (2017) The Psychology of Cows

Bacteria Mitigation In Sponge Mariculture, Jambiani Zanzibar, Claire Johnston

Independent Study Project (ISP) Collection

The declining seaweed industry coupled with efforts by the NGO Marine Cultures have led to the establishment of sponge mariculture in Jambiani, Zanzibar. However, growing cyanobacteria levels have substantially increased sponge mortality rates. In order to determine successful cyanobacteria mitigation treatments, six populations of farm ropes, support lines, and sponges were (a) untreated, (b) manually cleaned or submerged in solutions of (c) 2% hydrogen peroxide, (d) 4% hydrogen peroxide, (e) 50 g/L salt, or (f) 70 g/L salt. No conclusions were drawn from rope treatments, no techniques were effective for support line treatments, and both concentrations of hydrogen peroxide were …

Rehabilitation Of An Injured Golden Eagle (Aquila Chrysaetos): A Case Study, Fida Muhammad Khan, Fakhar-I- Abbas, Abu Ul Hassan Faiz

Journal of Bioresource Management

Habitat destruction and anthropogenic activities cause wild birds to migrate towards urban areas in search of food and sometimes nesting in high-roof buildings, where they are caught by local people using different techniques and are further used for hunting or recreational purposes. An injured Golden Eagle (Aquila chrysaetos) was found entangled in bushes near the vicinity of Balkasar Research Complex, Chakwal, Pakistan. After complete physical examination, a wound on the right wing and closed leg fracture was diagnosed. The successful treatment was done by anti-parasitic and anti-bacterial drugs with careful monitoring. Splint was adjusted after aligning the fractured …

T-Time: A Data Repository Of T Cell And Calcium Release-Activated Calcium Channel Activation Imagery, Cody Arbuckle, Milton L. Greenberg, Adrienne Bergh, Rene German, Nick Sirago, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

BACKGROUND: A fundamental understanding of live-cell dynamics is necessary in order to advance scientific techniques and personalized medicine. For this understanding to be possible, image processing techniques, probes, tracking algorithms and many other methodologies must be improved. Currently there are no large open-source datasets containing live-cell imaging to act as a standard for the community. As a result, researchers cannot evaluate their methodologies on an independent benchmark or leverage such a dataset to formulate scientific questions.

FINDINGS: Here we present T-Time, the largest free and publicly available data set of T cell phase contrast imagery designed with the …

Letter To The Editor, Jarrod Bailey

Validation of Animal Experimentation Collection

It seems clear that heeding the opinions and recommendations of experienced neuroscientists such as Professor Beuter, the well-argued probable opinion of the time-travelling Parkinson, and Grimm and Eggel’s demands for high animal welfare and honest and realistic harm–benefit analyses, will be of paramount importance for the advancement and evolution of experiments involving NHPs, particularly in neuroscience. This will benefit animals and humans alike.