Life Sciences Commons^™

Identification And Analysis Of Bacterial Genomic Metabolic Signatures, Nathaniel Bowerman, Nathan L. Tintle, Matthew Dejongh, Aaron A. Best

Faculty Work Comprehensive List

With continued rapid growth in the number and quality of fully sequenced and accurately annotated bacterial genomes, we have unprecedented opportunities to understand metabolic diversity. We selected 101 diverse and representative completely sequenced bacteria and implemented a manual curation effort to identify 846 unique metabolic variants present in these bacteria. The presence or absence of these variants act as a metabolic signature for each of the bacteria, which can then be used to understand similarities and differences between and across bacterial groups. We propose a novel and robust method of summarizing metabolic diversity using metabolic signatures and use this method …

Powerful Method For Including Genotype Uncertainty In Tests Of Hardy-Weinberg Equilibrium, Andrew Beck, Alexander Luedtke, Keli Liu, Nathan L. Tintle

Faculty Work Comprehensive List

The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack calibration in the type I error rate, especially as genotype uncertainty increases. We propose a new approach in the spirit of genomic control that properly calibrates the type I error rate, while yielding improved power to detect deviations from Hardy-Weinberg Equilibrium. We demonstrate the improved performance of our method on both …

Comparisons Of Isogenic Trisomic And Disomic Cells From People With Mosaicism For Down Syndrome Unmask Cellular Differences Related To Trisomy 21, Kelly A. Rafferty

Theses and Dissertations

It is known that age-related changes impacting multiple organ systems occur earlier in people with Down syndrome (Ds), but the biological basis underlying this trisomy 21-associated propensity for premature aging is poorly understood. Given that the trisomic/normal cells from people with mosaic Ds (mDs) are identical with regards to environmental exposures and genes (except for chromosome 21 copy number), comparisons of these isogenic trisomic/disomic cells allow one to “unmask” the cellular consequences of trisomy 21 by removing extraneous factors. The primary aim of this study was to determine if trisomy 21 results in an increase in the acquisition of age-related …

A Comparative Analysis Of Geometric Morphometrics Across Two Pseudemys Turtle Species In East Central Virginia, Kristin C. Dillard

Theses and Dissertations

The phylogeny of the turtle genus Pseudemys is poorly understood. In Virginia, many turtles have been found with indicator traits of both eastern river cooters (Pseudemys concinna concinna) and northern red bellied cooters (Pseudemys rubriventris). This study explores morphological evidence for hybridization between the two species across three riverine sites in east central Virginia.

Museum voucher groups for each species were analyzed for relative shell height and plastron length. The shape of the plastral scutes and upper jaw were analyzed using landmark-based morphometric software. These metrics were compared with measurements taken from 188 field-caught Pseudemys specimens. …

Quantifying Current Sediment Deposition, Legacy Sediments, And Pre-Impoundment Vertical Accretion And Carbon Dynamics Following Dam Removal In A Recently Restored Tidal Freshwater Wetland, Melissa J. Davis

Theses and Dissertations

Damming disrupts natural sediment flow to downstream resulting in legacy sediment accumulation. Legacy sediments have been well investigated in streams throughout the Piedmont region; however, there is no research of legacy sediments following dam removal in low-gradient Coastal Plain streams. Research objectives were to: characterize legacy sediments in a low-gradient stream restoration, quantify pre-impoundment accretion and carbon dynamics, and assess current sediment deposition rates via ¹⁴C analyses within sediment cores and sediment collection tiles. Carbon accumulation and accretion rates of modern tidal sediment have reached that of the tidal relic benchmark and current sediment deposition rates are similar between …

Pelagic Fish Diversity And Density On And Off Restored Oyster Reef Habitat, Danielle Mcculloch

Theses and Dissertations

The heterogeneity provided by structured habitats is important in supporting diverse and dense fish communities. The biogenic reefs created by the native Eastern Oyster, Crassostrea virginica, were once the dominant structural habitat in Chesapeake Bay, and have since declined to less than 1% of historic estimates. Conflicting results on the effects of oyster reef restoration on pelagic fish assemblages make further investigation necessary. Incorporating multiple sampling strategies may help elucidate oyster reef habitat influence on fish assemblages. This study used multi-panel gillnets, hydroacoustic technology, and day-night sampling to describe pelagic fish assemblages on and off oyster reef habitat in the …

A Study Of Critical Value Notification In The Outpatient Setting: The Relationship Between Physician Response And Patient Outcomes, Kristie Renee Finney

Theses and Dissertations

Critical values are laboratory values that represent a life-threatening condition for which there is a treatment available. Laboratories make immediate notifications to ordering providers when critical values are identified so that they may quickly act to initiate a treatment for their patient. The majority of laboratories apply the inpatient critical value list to the outpatient setting, although there are many differences between an acutely ill inpatient population and an ambulatory outpatient population. The goal of this study was to determine if providers responded to the critical values in the outpatient setting and to determine if there was a difference in …

Behavioral Responses Of Sub-Adult Atlantic Sturgeon (Acipenser Oxyrinchus Oxyrinchus) To Electromagnetic And Magnetic Fields Under Laboratory Conditions, Andrew Mcintyre Iii

Theses and Dissertations

Electromagnetic fields (EMF) produced by high voltage (HV), submarine transmission cables leading from offshore wind energy generation facilities could affect foraging or migratory behaviors of electro-receptive fishes, including endangered Atlantic Sturgeon. However, no published studies have quantitatively evaluated the possible behavioral effects of EMF exposure on sturgeon during residence in coastal waters. This study evaluated behavioral responses by sub-adult Atlantic Sturgeon to electromagnetic and magnetic fields under controlled laboratory conditions. Fabricated EMF generators were used to emulate a range of field EMF conditions that migratory fishes could encounter in proximity to submarine HV sources. Sensor arrays and digital video recorders …

Anti-Proliferative Effect Of Hibernating American Bullfrog, Lithobates Catesbeianus, Blood Plasma On The Thp-1 Cells, Sean L. Robbins

Dissertations and Theses @ UNI

Hibernation is a remarkable process that allows an organism to go dormant for long periods of time during the winter, when food is scarce and living conditions can be lethal. Much is unknown about the physiology behind hibernation, and most research comes from mammalian models. For example, it is known that during hibernation many of the cells in the body are impeded from going though mitosis but the mechanism that caused this was unknown. It was recently discovered that 13-lined ground squirrels (Ictidomys tridecemlineatus) and woodchucks (Marmota monax) have a protein, alpha-2-macroglobulin, in their blood plasma, …

Reducing The Rate Of Late Stage Breast Cancer Through Effective Health Communication: An Opinion Piece, Rachele Hendricks-Sturrup

Internet Journal of Allied Health Sciences and Practice

Purpose: Health and illness are traditionally characterized and treated differently across various ethnic groups, which encourages American health systems serving these diverse populations to explore culturally competent and safe ways to effectively reduce illness within such populations. Certain ethnic groups of women in the United States (US) bear greater risk of late stage breast cancer because of various circumstances, which include but are not limited to a lack of insurance or underinsurance and discomfort with and/or resentment toward the US healthcare system. The dominant culture and the social aspects of the modern American health system often and most favorably serve …

Individual Fluid Plans Versus Ad Libitum On Hydration Status In Minor Professional Ice Hockey Players, Dawn M. Emerson, Toni Torres-Mcgehee, Charles C. Emerson, Teri L. Lasalle

Faculty Publications

BACKGROUND: Despite exercising in cool environments, ice hockey players exhibit several dehydration risk factors. Individualized fluid plans (IFPs) are designed to mitigate dehydration by matching an individual's sweat loss in order to optimize physiological systems and performance. METHODS: A randomized control trial was used to examine IFP versus ad libitum fluid ingestion on hydration in 11 male minor professional ice hockey players (mean age = 24.4 ± 2.6 years, height = 183.0 ± 4.6 cm, weight = 92.9 ± 7.8 kg). Following baseline measures over 2 practices, participants were randomly assigned to either control (CON) or intervention (INT) for 10 …

Museum Collections: Natural History Training Bridges Time, Space, And Digital Platforms., Anna Monfils, Karen Powers, Christopher J. Marshall, James F. Smith, Chris Martine, L. Alan Prather

Faculty Journal Articles

Natural history collections offer a number of unique physical and virtual opportunities to create formal and informal progressive learning environments. Collections provide direct interaction with biodiversity as it changes through time and space. Collections-based experiences lead to an increased understanding and substantive interaction with the living world. Recent studies demonstrate how nature and outdoor experiences can improve learning. We discuss how collections, and the data associated with collections, are a critical component linking nature and scientific inquiry. Partnerships that develop around collections and collections-based science can foster innovative educational and research experiences that are enhanced by access to museum specimens. …

Marine Mammal Tracks From Two-Hydrophone Acoustic Recordings Made With A Glider, Elizabeth T. Küsel, Tessa Munoz, Martin Siderius, David K. Mellinger, Sara L. Heimlich

Electrical and Computer Engineering Faculty Publications and Presentations

A multinational oceanographic and acoustic sea experiment was carried out in the summer of 2014 off the western coast of the island of Sardinia, Mediterranean Sea. During this experiment, an underwater glider fitted with two hydrophones was evaluated as a potential tool for marine mammal population density estimation studies. An acoustic recording system was also tested, comprising an inexpensive, off-the-shelf digital recorder installed inside the glider. Detection and classification of sounds produced by whales and dolphins, and sometimes tracking and localization, are inherent components of population density estimation from passive acoustics recordings. In this work we discuss the equipment used …

Women In Science 2017, Clark Science Center's Summer Research Fellows Program

SURF Abstracts (Women in Science)

Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. Women in Science 2017 summarizes research done by Smith College’s SURF Program participants during the summer of 2017. 151 students participated in SURF (144 hosted on campus and nearby eld sites), supervised by 58 faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants summarized their research experiences for this publication.

Factors Affecting Growth Rates And Preferred Body Temperatures In Hatchling Gopher Tortoises, Gopherus Polyphemus: Clutch And Sex, Matthew Carey

College of Graduate Studies: Theses & Dissertations

Post hatching growth rates in tortoises can affect size at sexual maturity This study looks at what affect clutch and sex has on hatchling tortoises from these two sites as this data is lacking/insufficient from two populations in Southeast Georgia. Eggs were allowed to incubate in natural nests and then were collected between August 19-21, 2015 and hatched in an incubator in the lab. When they hatched, the tortoises were kept in a single room with a rearing temperature that averaged 26.9° C. Sex was determined using laparoscopy at the end of the study to ensure gonad development and to …

Bioanalysis For Cocaine, Opiates, Methadone And Amphetamines Exposure Detection During Pregnancy, Marta Concheiro, Elena Lendoiro, Ana De Castro, Eva Gonzalez-Colmenero, Ana Concheiro-Guisan, Patricia Penas-Silva, Manuel Macias-Cortina, Angelines Cruz-Landeira, Manuel Lopez-Rivadulla

Publications and Research

Drug exposure during pregnancy constitutes a major legal issue and public health concern. Drug and metabolite determination in biological matrices from mother and newborn is an objective indication of prenatal drug exposure. However, limited data are available regarding the interpretation of these analytical results in terms of window of detection and degree of exposure. We collected paired maternal hair, meconium, placenta and umbilical cord from 727 mother-newborn dyads. We analyzed these specimens by liquid chromatography tandem mass spectrometry for the determination of cocaine, opioids, methadone and amphetamines, and compared the analytical results from the four different matrices. The cases were …

Expanding Our Understanding Of The Trade In Marine Aquarium Animals, Andrew L. Rhyne, Michael F. Tlusty, Joseph T. Szczebak, Robert J. Holmberg

Arts & Sciences Faculty Publications

The trade of live marine animals for home and public aquaria has grown into a major global industry. Millions of marine fishes and invertebrates are removed from coral reefs and associated habitats each year. The majority are imported into the United States, with the remainder sent to Europe, Japan, and a handful of other countries. Despite the recent growth and diversification of the aquarium trade, to date, data collection is not mandatory, and hence comprehensive information on species volume and diversity is lacking. This lack of information makes it impossible to study trade pathways. Without species-specific volume and diversity data, …

The Central Arctic Ocean-Preventing Another Tragedy Of The Commons, Andrew J. Norris, Patrick Mckinley

Arts & Sciences Faculty Publications

Arctic sea ice is melting, slowly but inexorably. As the ice disappears, mankind will be afforded access to regions and activities, including commercial fishing, that have been inaccessible for our entire recorded history. There is currently no regulatory body or mechanism in the high seas Arctic (also referred to as the central Arctic Ocean) to conserve and manage fish stocks, the distribution and concentration of which are poorly understood, and that might be the target of commercial fisheries. This article examines the extent and nature of ice recession in the Arctic, and its likely effect on the accessibility of central …

Season, But Not Symbiont State, Drives Microbiome Structure In The Temperate Coral Astrangia Poculata., Koty H. Sharp, Zoe A. Pratte, Allison H. Kerwin

Arts & Sciences Faculty Publications

BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome …

Crassulacean Acid Metabolism As A Continuous Trait: Variability In The Contribution Of Crassulacean Acid Metabolism (Cam) In Populations Of Portulacaria Afra, Lonnie J. Guralnick, Kate Gladsky

Arts & Sciences Faculty Publications

Portulacaria afra L. is a dominant facultative CAM species growing in the Southeastern Cape of South Africa. P. afra is well adapted to regions of the Spekboom thicket in areas of limited and sporadic rainfall. P. afra populations occur in isolated drainages. We hypothesized the utilization of CAM would vary in the different populations in response to rainfall and temperature gradients. Carbon isotope composition can be used to determine the contribution of CAM in leaf tissue. P. afra leaves of populations were analyzed in transects running south to north and east to west in locations from the coast to elevations …

Carbon Dioxide Sources From Alaska Driven By Increasing Early Winter Respiration From Artic Tundra, Roisin Commane, Jacob Lindaas, Joshua Benmergui, Kristina Luus, Rachel Chang, Bruce Daube, Eugenie Euskirchen, John Henderson, Anna Karion, John Miller, Scot Miller, Nicholas Parazoo, James Randerson, Colm Sweeney, Pieter Tans, Kirk Thoning, Sander Veraverbeke, Charles Miller, Steven Wofsy

Articles

High-latitude ecosystems have the capacity to release large amounts of carbon dioxide (CO2) to the atmosphere in response to increasing temperatures, representing a potentially significant positive feedback within the climate system. Here, we combine aircraft and tower observations of atmospheric CO2 with remote sensing data and meteorological products to derive temporally and spatially resolved year-round CO2 fluxes across Alaska during 2012-2014. We find that tundra ecosystems were a net source of CO2 to the atmosphere annually, with especially high rates of respiration during early winter (October through December). Long-term records at Barrow, AK, suggest that CO2emission rates from North Slope …

Extraction And Quantification Of Sinapinic Acid From Irish Rapeseed Meal And Assessment Of Angiotensin-I Converting Enzyme (Ace-I) Inhibitory Activity, Leah Quinn, Steven G. Gray, Steve Meaney, Stephen Finn, Padraig Mcloughlin, Maria Hayes

Articles

Phenolic compounds, including phenolic acids, are known to play a protective role against the development of cardiovascular disease. The aim of this work was to generate a phenolic acid extract from Irish rapeseed meal, to determine the quantity of sinapinic acid (SA) in this fraction and to assess the ability of this fraction to inhibit the enzyme angiotensin-I converting enzyme (ACE-I; EC 3.4.15.1). A crude phenolic extract (fraction 1), free phenolic acid containing extract (fraction 2), and an extract containing phenolic acids liberated from esters (fraction 3) were generated from Irish rapeseed meal using a methanol:acetone:water solvent mixture (7:7:6). The …

1,10-Phenanthroline-5,6-Dione-Based Compounds Are Effective In Disturbing Crucial Physiological Events Of Phialophora Verrucosa, Marcela Queiroz Granato, Diego De Souza Goncalves, Sergio Henrique Seabra, Malachy Mccann, Michael Devereux, Andre Luis De Souza Dos Santos, Lucimar Ferreira Kneipp

Articles

Phialophora verrucosa is a dematiaceous fungus able to cause chromoblastomycosis, phaeohyphomycosis and mycetoma. All these fungal diseases are extremely difficult to treat and often refractory to the current therapeutic approaches. Therefore, there is an urgent necessity to develop new antifungal agents to combat these mycoses. In this context, the aim of the present work was to investigate the effect of 1,10-phenanthroline-5,6-dione (phendione) and its metal-based derivatives [Ag(phendione)2]ClO4 = ([Ag(phendione)2]+) and [Cu(phendione)3](ClO4)2.4H2O = ([Cu(phendione)3]2+) on crucial physiological events of P. verrucosa conidial cells. Using the CLSI protocol, we have shown that phendione, [Ag(phendione)2]+ and [Cu(phendione)3]2+ were able to inhibit fungal proliferation, …

Rapid Turnover Of Ciliate Community Members In New England Tide Pools, Mary Badger, Sarah J. Tucker, Jean-David Grattepanche, Laura A. Katz

Biological Sciences: Faculty Publications

The rocky intertidal zone represents a dynamic habitat marked by considerable species richness, which has been well-documented for invertebrates and macroalgae. This high biodiversity exists in the context of extreme fluctuations in abiotic factors such as temperature, salinity and pH that occur during each tidal cycle. Despite these attributes, few studies have focused on microbial diversity in tide pools, including analyses of the ciliate communities that are the focus of this study. We investigated the spatial and temporal distributions of ciliate species across the intertidal environment at sites in Maine and Connecticut, USA. Our study used a DNA fingerprinting technique, …

Dissonance Reduction In Nonhuman Animals: Implications For Cognitive Dissonance Theory, Cindy Harmon-Jones, Nick Haslam, Brock Bastian

Animal Sentience

We review the evidence for dissonance reduction in nonhuman animals and examine the alternative explanations for these effects. If nonhuman animals engage in dissonance reduction, this supports the original theory as proposed by Festinger (1957) over the revisions to the theory that focused on the self-concept. Evidence of animal sentience, including dissonance reduction, may be a source of cognitive dissonance.

Clarifying Concepts In Cognitive Dissonance Theory, Eddie Harmon-Jones

Animal Sentience

This commentary on Zentall’s target article focuses primarily on clarifying some postulates and variables in cognitive dissonance theory. I discuss the adaptive motivational functions of dissonance arousal and dissonance reduction, and attempt to clarify some past dissonance experiments and to tease apart a dissonance theory and contrast explanation of effort-justification-type effects. The evidence and arguments reviewed here support the explanatory power of cognitive dissonance theory in a wide variety of circumstances in human and nonhuman animals, but they depend on first defining concepts such as “cognitions” quite broadly, as Festinger did when he originally proposed the theory.

The Potential For Sentience In Fishes, Jay R. Stauffer Jr.

Animal Sentience

Balcombe’s book is filled with information on the biology, behavior, and life history of fishes. I do not agree with all his premises. I am still somewhat perplexed about the discussion of whether fish feel pain; I am not sure whether the distinction between nociception and pain makes any difference. Overall, however, his treatment of the principles of both natural and sexual selection is comprehensive and accurate, and has greatly increased my knowledge and awareness of the biology, ethology, and potential for sentience in fishes. In summary, this work has exposed me to new ideas about how to examine fishes …

Identification Of Proteins Differentially Accumulated In Enterococcus Faecalis Under Acrylamide Exposure, Aleksandra Bocian, Konrad Hus, Marcin Jaromin, Miroslaw Tyrka, Andrzej Lyskowski

Turkish Journal of Biology

Analysis of bacterial proteomes can be used to obtain large amounts of information about adaptive microbial mechanisms to changing extracellular conditions. In the past, many bacterial species with the ability to degrade acrylamide were isolated. In this study differences in the Enterococcus faecalis proteome upon acrylamide exposure were investigated. We revealed substantial changes in the proteome of bacteria cultured in different environmental conditions. Microorganisms exposed to acrylamide showed higher accumulation of proteins associated with energy metabolism and its regulation. Moreover, several proteins involved in protection of cells from stress conditions were also identified. These biomacromolecules are involved in proper folding …

Converted Carotenoid Production In Dunaliella Salina By Using Cyclization Inhibitors 2-Methylimidazole And 3-Amino-1,2,4-Triazole, Arzu Yildirim, İsmai̇l Hakki Akgün, Meltem Dalay

Turkish Journal of Biology

Carotenoids are vital for most photosynthetic organisms because of their crucial role in prevention of the damage caused by excess light or stress conditions like heat or nutrient deprivation. Some of them are also valuable for biotechnology wıth respect to their colorful feature and antioxidant properties. In this study, a natural β-carotene producer, green microalga Dunaliella salina, was evaluated for its potential to produce different valuable carotenoids through the inhibition of cyclization reactions in the carotenoid pathway by the chemical inhibitors 2-methylimidazole (2MI) and 3-amino-1,2,4-triazole (Amitrol). 2MI was shown to be effective on lutein accumulation in D. salina cultures grown …

Cotesia Icipe Sp. N., A New Microgastrinae Wasp (Hymenoptera, Braconidae) Of Importance In The Biological Control Of Lepidopteran Pests In Africa, Komi K.M. Fiaboe, Jose Fernández-Triana, Faith W. Nyamu, Komi M. Agbodzavu

All Peer-Reviewed Publications

A new species of Microgastrinae, Cotesia icipe Fernández-Triana & Fiaboe, sp. n., is described from eastern Africa. It was reared in Kenya as a solitary parasitoid from two major amaranth pests, Spodoptera littoralis (Boisduval, 1833) and S. exigua (Hübner, 1808); study of specimens in collections also revealed its presence in four other countries in the Afrotropical region (Madagascar, Saudi Arabia, South Africa, and Yemen). Morphological, molecular and biological characters are used to describe the new species and to distinguish it from all 12 previously described species of Afrotropical Cotesia. Cotesia icipe shows potential in the biological control of key Lepidopteran …