Laboratory and Basic Science Research Commons^™

Using Active Learning To Build A Foundation For Bioinformatics Training., Stacey E. Wahl Ph.D., Amy L. Olex Ms

Transforming Libraries for Graduate Students

As Health Sciences Libraries evolve, the support they offer graduate students has evolved to incorporate many aspects of the research life cycle. At Tompkins-McCaw Library for the Health Sciences, we have partnered with the Wright Center for Clinical and Translational Research to offer training workshops for graduate students who are interested in using bioinformatics to plan, analyze, or execute scientific experiments. We offer two series: 1) an 8-week, 1-hour per week seminar series providing a general overview of available techniques and 2) a week-long intensive, two hours per session, series on utilizing free databases from the National Center for Biotechnology …

Valorization Of Carrot Processing Waste, Alexandra M. Duval

Master's Theses

Commercial carrot processors produce up to 175,000 tons of carrot waste annually. Carrot Mash (CM) is the term referring to the waste by-product of peeled baby carrot processing. Transportation of carrot processing waste is expensive due to its high- water content (approx. 83-95%). High in bioactive compounds (carotenoids) and dietary fibers, it is expected that its conversion into a value-added by-product is of interest to the carrot processing industry. Hemicellulose-rich plant materials have proven to be a source of oligosaccharides, which are known for their beneficial prebiotic activity. The objectives of this research were to: 1) determine the effect of …

Polyphenol-Rich Purple Corn Pericarp Extract Adversely Impacts Herbivore Growth And Development, Mandeep Tayal, Pavel Somavat, Isabella Rodriguez, Tina Thomas, Bradley O. Christoffersen, Rupesh R. Kariyat

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Plant secondary metabolites such as terpenes, phenolics, glycosides, and alkaloids play various functional roles including pigmentation, foliar and floral volatile synthesis, hormonal regulation, and direct and indirect defenses. Among these, phenolic compounds are commonly found in plants, but vary in the distribution of their specific compounds among plant families. Polyphenols, including anthocyanins and tannins, are widely distributed and have been well documented for their roles- primarily in plant pigmentation and also in plant defenses. However, commercialization of such compounds for use in insect pest management is severely hampered by expensive, inefficient, and time-consuming extraction protocols. Using a recently developed inexpensive …

A Review Of The Scientific Rigor, Reproducibility, And Transparency Studies Conducted By The Abrf Research Groups., Sheenah M Mische, Nancy C Fisher, Susan M Meyn, Katia Sol Church, Rebecca L Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M Ashton, Kym M Delventhal, Julie A Dragon, Laura Holmes, Pratik Jagtap, Christopher E Mason, Magnus Palmblad, Brian C Searle, Christoph W Turck, Kevin L Knudtson

Articles, Abstracts, and Reports

Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and thedy have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific …

Water In Your Neighbourhood: A Model For Implementing A Semester-Long Course-Based Undergraduate Research Project In Introductory Biology, Ana Lucia Fuentes, Maria Entezari

Publications and Research

Undergraduate biology education has changed over the past decade, incorporating an iterative and evidence-based approach. Many educational assessments have confirmed the effectiveness of integrating authentic research and open-ended inquiry into introductory biology courses, demonstrating a significant positive impact on students’ learning and attitude towards STEM majors. Despite these findings, only a handful of Biology instructors in 2-year colleges adopt this approach, and when adopted, most activities constitute a small fraction of these courses. Finding a feasible, sustainable, semester-long, and cost-effective strategy to incorporate authentic research in the curriculum which promotes integrated understanding of science and addresses socio-scientific issues, is a …

Using Northern Pike And Yellow Perch To Attempt A Trophic Cascade, Bryan Sea

Journal of Earth and Life Science

In the midwestern USA, water clarity has decreased in shallow lakes as a result of large populations of Fathead Minnow Pimephales promelas and agriculture that impact the life that depend on shallow habitats, such as waterfowl, fish, and aquatic plants. Northern Pike Esox lucius and Yellow Perch Perca flavescens were stocked in a few lakes in attempt to create a tropic cascade and reduce populations of nuisance Fathead Minnows. Northern Pike were stocked as fry and Yellow Perch were stocked as adults either pre-spawn or post-spawn. Lake managers hypothesized adult Yellow Perch would spawn and the age-0 Perch would feed …

Focal Augmentation Of Somatostatin Interneuron Function And Subsequent Circuit Effects In Developmentally Malformed, Epileptogenic Cortex, Nicole Ekanem

Theses and Dissertations

Drug-resistant epilepsy (DRE) is a common clinical sequela of developmental cortical malformations such as polymicrogyria. Unfortunately, much remains unknown about the aberrant GABA-mediated circuit alterations that underlie DRE's onset and persistence in this context. To address this knowledge gap, we utilized the transcranial freeze lesion model in optogenetic mice lines (Somatostatin (SST)-Cre or Parvalbumin (PV)-Cre x floxed channelrhodopsin-2) to dissect features of the SST, PV, and pyramidal neuron microcircuit that are potentially associated with DRE. Investigations took place within developmental microgyria’s known pathological substrate, the adjoined and epileptogenic paramicrogyral region (PMR). As well, microcircuit relationships within the previously unexplored range …

Solid Phase Extraction And High-Precision Mass Spectrometry Analysis Methods For Crassostrea Virginica Metabolome, Alyssa Darling

Theses and Dissertations

Metabolomics is the rapidly-growing field which focuses on the endpoints of biological processes, and has the capability to provide a snapshot of an organisms’ interaction with their environment on a molecular scale. The objective of the experiment herein was to develop a standard metabolic extraction technique coupled with ultrahigh-precision analytical tools to build a global metabolic pathway of the keystone species Crassostrea virginica. To achieve this, C. virginica whole-body samples were extracted using acetonitrile and methanol, then split into a dehydrated group and a diluted group. Following reversed-phase solid phase extraction (RP-SPE) of both groups, metabolites were identified using …

Tick-Borne Infections In New Hampshire: An Evaluation Of The Diagnostic Process In A Local Patient Population, Katherine Anderson

Honors Theses and Capstones

Overall, approximately 95 percent of reported cases of vector-borne disease were associated with ticks, making these the most medically important group of arthropods in the United States.¹ Despite the prevalence of tick-borne infections, the process for the diagnosis of this condition is not well studied. This study aims to analyze data from a pool of 100 patients who underwent testing for tick-borne disease in the same institution in Dover, New Hampshire during the most recent peak tick season of 2019. Information utilized in this study included: patient age, sex, location of testing (inpatient versus outpatient), diagnostic testing methods used …

Correlating The Physicochemical Properties Of Magnesium Stearate With Tablet Dissolution And Lubrication, Julie L. Calahan

Theses and Dissertations--Pharmacy

Magnesium stearate (MgSt) is the most commonly used pharmaceutical excipient and is present in over half the tablet formulations on the market. In spite of its popularity as an effective lubricant, it has been repeatedly recognized that there is significant variability between MgSt samples, which can cause inconsistent lubrication between batches of MgSt. The hypothesis of this research is that the batch-to-batch variability in tablet lubrication and dissolution observed in tablet formulations containing different MgSt samples can be correlated with differences in MgSt physicochemical properties (fatty acid salt composition, crystal hydrate form, particle size and surface area). Developing correlations between …

Walleye Sander Vitreus Visceral Fat Accumulation, Cole Daleiden, Seth Renner

Journal of Earth and Life Science

For ectothermic species, proper lipid retention is critical to surviving in regions with limited growing seasons. Visceral fat is the dominant form of this energy storage in fish. Build up and depletion of these lipids occur seasonally as activity levels change throughout winter and spring. Due to this annual pattern, the purpose of this study is to determine a trend in the amount of visceral fat Walleye Sander vitreus accumulate in a time of year when metabolic rates are low and transition into the spawning process has yet to occur. Angling was the method of capture conducted during the months …

Diffusion And Osmosis: Passive Movement Of Molecules In Biological Systems, Ana Lucia Fuentes, Maria Entezari

Open Educational Resources

During this lab, students determine the salinity of collected water samples. They also compare the effect of the solute concentration of their samples with that of solutions of known solute concentrations on plant cells.

The Cardiovascular Response To Acute Hypoxic Conditions In Danio Rerio, Bryce Fetterman

Williams Honors College, Honors Research Projects

There are many fish that can withstand hypoxia levels. One in particular is the zebrafish (Danio rerio). The zebrafish is a small-sized, Cyprinid teleost fish, and has been used in a laboratory setting for many reasons. A few reasons being that they are widely available, easy to care for, and the cost for these fish are very low. There are various reasons why these fish are used as a model. One main reason is because their cardiovascular system is one of the first developing organs. This allows for better resolution when studying the cardiovascular system. The purpose of …

Determination Of Iron-Reducing Bacterial Activities In Lake Sediments., Alexandra Kahn

Williams Honors College, Honors Research Projects

Algal blooms are growing rampantly in lacustrine systems due to an increase of phosphorus, a nutrient for algae. Phosphorus is being released into the environment causing overpopulation and eutrophication which damages the ecosystem. The availability of phosphorus is affected by the solubility of iron which is regulated through iron reducing and iron oxidizing bacteria. Phosphorus adheres to insoluble Fe(III), which prohibits algae from utilizing it, while phosphorus does not attach to soluble Fe(II) and therefore it remains available to algae. The purpose of this study was to determine how bacteria influence iron solubility and what are the ideal environmental conditions …

Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan Mcnamara

Williams Honors College, Honors Research Projects

I tested the hypothesis that recombinant leptin protein can be introduced to zebrafish in vivo through non-invasive soaking in a solution containing the protein. One way to study various molecules’ effects in vivo is through intraperitoneal or intracerebroventricular injections during the embryonic or larval stage, which is invasive, difficult to administer, and can have a high mortality rate. 48 hours post fertilization (hpf) zebrafish were soaked in a His-tagged recombinant leptin protein solution at 10 nM and 100 nM concentrations (produced by Genscript). After soaking, zebrafish larvae were washed extensively to remove all recombinant protein on their exterior before homogenization. …

Kidney Stone Analysis And Spiritual Guides (Pir Faqir): The Known-Unknowns, Lena Jafri, Aysha Habib Khan, Humaira Asif

Department of Pathology and Laboratory Medicine

No abstract provided.

Glycogen Storage Diseases-Time To Flip The Outdated Diagnostic Approach Centered On Liver Biopsy With The Molecular Testing, Sibtain Ahmed, Bushra Afroze

Department of Pathology and Laboratory Medicine

The glycogen storage diseases (GSDs) are a group of inherited metabolic disorders that result from a defect in any one of several enzymes required for either glycogen synthesis or glycogen degradation. The traditional diagnostic approach is based on the invasive hepatic or muscle biopsies, which are neither cost effective nor convenient. Molecular (gene testing) has emerged over the course of past few years as a robust alternative diagnostic tool, which not only confirms the diagnosis of GSDs but also clearly differentiates the types of GSDs allowing the initiation of the type-specific appropriate treatment for the particular type of GSDs. The …

Antifungal Defense Molecules From Bacterial Symbionts Of North American Trachymyrmex Ants, Georgia Scherer

CMC Senior Theses

Defensive symbioses, in which microbes provide molecular defenses for an animal host, hold great potential as untapped sources of therapeutically useful antibiotics. Fungus-growing ants use antifungal defenses from bacterial symbionts to suppress pathogenic fungi in their nests. Preliminary chemical investigations of symbiotic bacteria from this large family of ants have uncovered novel antifungal molecules with therapeutic potential, such as dentigerumycin and selvamicin.

In this study, the bacterial symbionts of North American Trachymyrmex fungus-growing ants are investigated for antifungal molecules. Plate-based bioassays using ecologically-relevant fungal pathogens confirmed that these bacteria have antifungal activity. In order to purify and identify the antifungal …

Biomechanics And Neural Control Of Movement: Cmi's Effects On Downstream Motor Processing And Gait In Forwards And Backwards Walking, Christopher Choi

CMC Senior Theses

Analyzing the effects of cognitive motor interferences (CMI) on walking is usually done in patients with neurological comorbidity or during forward walking (FW). However, there are few studies that examine gait differences between FW and backward walking (BW) under the presence of CMI when speed is kept constant on a treadmill. In this study we examined how CMI would disrupt sensory feedback and affect the descending motor pathway. We hypothesized that subjects that walked backwards and were given a cognitive task would show the greatest differences in gait due to a lack of visual input and the presence of CMI. …

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry …

Sindbis Virus Infects Specific Gut Cells For Replication And Dissemination From The Posterior Midgut Of Mosquitoes, Yani P. Ahearn

UNF Graduate Theses and Dissertations

Abstract

Sindbis virus (SINV), a member of the genus Alphavirus, is the protype virus used to gain insight into other disease-causing Alphaviruses. As a mosquito-borne-virus (arbovirus), SINV transit in adult female mosquitoes includes attachment to the gut lumen and entry into the midgut cells, followed by replication and dissemination into the hemolymph through yet unknown specific mechanisms. Free-mated adult females, aged day 5-7, were fed a viremic bovine blood suspension via blood sausage at a final SINV titer at 107 PFU/ml. Midguts from fully engorged mosquitoes were dissected on day 5 and 7 post-bloodmeal and further examined by immunolabeling using …

Role Of Nurd In Acute Leukemia Cell Survival, Javeria Aijaz

Theses and Dissertations

Depletion of the ATPase component of the Nucleosome Remodeling and Deacetylase (NuRD) complex, CHD4, reduces acute myeloid leukemia (AML) cell survival. This study identified other NuRD components, as potential therapeutic targets for disrupting protein-protein interactions within NuRD. In addition to AML, we established that T-cell Acute Lymphoblastic Leukemia (T-ALL) cell lines responded similarly to CHD4 depletion.

Greater than 90% depletion of either MBD2 or MBD3 (the mutually exclusive two DNA binding NuRD paralogues) – was unremarkable, but complete depletion of MBD3 increased apoptosis and genotoxic sensitivity. Combined depletion of MBD-NuRD proteins augmented apoptosis observed with complete MBD3 depletion - indicating …

The Impact Of Aging And Mechanical Injury On Alveolar Epithelial And Macrophage Responses In Acute Lung Injury And Inflammation, Michael S. Valentine

Theses and Dissertations

Patients with severe lung pathologies, such as Acute Respiratory Distress Syndrome (ARDS), often require mechanical ventilation as a clinical intervention; however, this procedure frequently exacerbates the original pulmonary issue and produces an exaggerated inflammatory response that potentially leads to sepsis, multisystem organ failure, and mortality. This acute lung injury (ALI) condition has been termed Ventilator-Induced Lung Injury (VILI). Alveolar overdistension, cyclic atelectasis, and biotrauma are the primary injury mechanisms in VILI that lead to the loss of alveolar barrier integrity and pulmonary inflammation. Stress and strains during mechanical ventilation are believed to initiate alveolar epithelial mechanotransduction signaling mechanisms that contribute …

Spinal Motor Neuron Excitability And Balance Control Changes Following Downslope Walking, Nikki Aitcheson-Huehn

Theses and Dissertations (Comprehensive)

Downslope walking (DSW) has been proposed as a rehabilitation tool for people with Multiple Sclerosis (PwMS) although there are mixed findings in young adults (YA) regarding the balance control changes, despite both populations experiencing depressed spinal motor neuron (MN) pool excitability. Our aim was to determine whether YAs could demonstrate improved balance control in conjunction with SOL H reflex depression (estimate of spinal MN excitability) following DSW. We also aimed to determine whether reciprocal inhibition was a potential mechanism for H reflex depression via conditioned SOL H reflexes. Thirty young adults (23±1.4y, 6 males) were assigned to 30-minutes of DSW …

Influence Of Salinity On Copper-Ligand Formation Constants, Fatimah Barnawi

Theses and Dissertations (Comprehensive)

Natural Organic Matter (NOM) is known to reduce metal, such as copper, toxicity in aquatic environments. Copper is essential for organisms, but elevated concentrations of dissolved copper can potentially be toxic. The toxicity of copper is related to its bioavailability, which is influenced by toxicity modifying factors, such as NOM (quantified as Dissolved Organic Carbon (DOC) in mg C/L), alkalinity, pH and major cation and anion concentrations. The principles are the same for fresh and saltwater, but the influence of high salt concentrations, such as in estuaries, and associated activity corrections, can modify NOM complexation of metals (i.e., modify logK …

Acclimation, Long-Term Repeatability, And Phenotypic Correlations Of Aerobic Metabolic Traits In The Gulf Killifish, Fundulus Grandis, Jessica E. Reemeyer

LSU New Orleans Theses and Dissertations

This research examined the effects of acclimation to lowered salinity, elevated temperature, and hypoxia on aerobic metabolism of the Gulf killifish, Fundulus grandis, a common estuarine resident of the Gulf of Mexico. Standard metabolic rate (SMR), maximum metabolic rate (MMR), absolute aerobic scope (AAS), and critical oxygen tension (P_crit) were each influenced by one or more acclimation treatments. Assessing the consistency of these traits measured in the same individuals over time, all were found to be significantly repeatable with no indication that the repeatability of any traits was affected by acclimation conditions. Significant correlations were found between …

Green Roof System Integrated Soil Methods, Jude R. Vallon, Ivan L. Guzman

Publications and Research

Large metropolitan areas like NYC are seeking to integrate sustainability into retrofitting buildings for the development of green infrastructure. Among the many environmental issues of urbanization, the UHI (urban heat island) effect and storm water runoff are of particular interest when it comes building structures. Individual buildings can contribute towards mitigating these effects with implementation of vegetative rooftops, i.e. Green Roofs. Commercial buildings are currently receiving government incentives and new constructions are required to include green roof installations. However, if existing buildings are considering the addition of a green roof on an existing roof, they have to factor in the …

Inhibition Of Serine, Glycine, One-Carbon Metabolism Reduces Proinflammatory Response, Ashlynn Mccall

Honor’s College Freeman Research Journal

Acute lung injury affects around 200,000 critically ill patients annually, with a mortality rate near 33%. With a lack of targeted therapies, it is vital to discover and understand the fundamental cellular processes that drive macrophage inflammation. In the field of macrophage immunometabolism, it is accepted that macrophages upregulating glycolysis indicates a role in proinflammatory processes, however, there is a lack of knowledge surrounding the intermediate pathways in glycolysis. This study examined the effects of serine, glycine, one-carbon metabolism inhibition on LPS-induced inflammation in bone marrow-derived macrophages. We show that the enzymatic expression of PHGDH and PSATl is unaffected when …

Categorization Of Vocal Fry In Running Speech, Katherine Proctor

Honors Projects

The purpose of this study was to examine and categorize patterns of vocal fry in running speech. Since no other research studies have attempted to fully categorize vocal fry before, and due to the universality of the phenomenon of vocal fry, and the potential psychosocial and voice disorder consequences that come with using it, this topic is of great significance. For this study, voice samples were read into Praat and analyzed, and minor differences in the physiologies that produce different “types” of fry were examined.Temporal categories of vocal fry discovered were as follows: “onset,” “earlier,” “later,” and “final,” depending on …

Staphylococcus Aureus Resistance Patterns In Wisconsin: 2018 Surveillance Of Wisconsin Organisms For Trends In Antimicrobial Resistance And Epidemiology (Swotare) Program Report, Rebecca H. Schulte, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Objective: Surveillance of antimicrobial resistance patterns on a local level can reveal paradigms not obvious on a regional or national scale. Data collection from this perspective may potentially impact local prescribing patterns and empiric treatment guidelines. The objective of this study was to establish a baseline Staphylococcus aureus antibiogram for the state of Wisconsin and to elucidate potential geographic and demographic factors associated with antimicrobial resistance.

Design: Multi-center laboratory surveillance, with testing at a single site utilizing standardized media and susceptibility testing protocols.

Methods: 309 isolates of clinically-significant S. aureus were collected from hospital microbiology laboratories across Wisconsin in 2018, …