Organisms Commons^™

Identification Of The Staphylococcal Cassette Chromosome Mec (Sccmec) Element In Viral Fractions From Environmental Samples, Emily M. Pelto

Senior Honors Projects, 2010-2019

Antibiotic resistance attributed to methicillin-resistant Staphylococcus aureus (MRSA) has become a growing concern over the last decade in both the healthcare and agricultural environment. This resistance is encoded by the gene mecA that is located on a mosaic, mobile genetic element called the Staphylococcal Cassette Chromosome mec (SCCmec) element. It is proposed that the transfer of the SCCmec element and resulting spread of resistance occur by transduction, the transfer of genetic material from bacterium to bacterium by a bacteriophage. Specifically, it is hypothesized that the transduction of this resistance is occurring in the agricultural setting. To test …

Construct Validity Of Animal-Assisted Therapy And Activities: How Important Is The Animal In Aat?, Lori Marino

Lori Marino, PhD

Animal-assisted therapy and animal-assisted activities involve a nonhuman animal as a key therapeutic agent in some kind of intervention that may range from highly specified, as in AAT, to more casual, as in AAA. In this review I address the question: How important is the animal in animal therapy? In other words, does the recent literature strongly support the notion that a live animal, as opposed to another novel stimulating component, is specifically necessary for therapeutic success. Two meta-analyses and 28 single empirical studies were reviewed in order to address this issue. I conclude that the effects of AAT and …

Effect Of Novel Dietary Supplement On Metabolism In Vitro And In Vivo, Robert A. Vaughan, Ailish C. White, Jason R. Beam, Nicholas P. Gannon, Randi Garcia-Smith, Roy M. Salgado, Marco Bisoffi, Kristina A. Trujillo, Carole A. Conn, Christine M. Mermier

Health Sciences and Kinesiology Faculty Articles

Obesity is an increasingly prevalent and preventable morbidity with multiple behavioral, surgical and pharmacological interventions currently available. Commercial dietary supplements are often advertised to stimulate metabolism and cause rapid weight and/or fat loss, although few well-controlled studies have demonstrated such effects. We describe a commercially available dietary supplement (purportedly containing caffeine, catechins, and other metabolic stimulators) on resting metabolic rate in humans, and on metabolism, mitochondrial content, and related gene expression in vitro. Human males ingested either a placebo or commercially available supplement (RF) in a randomized double-blind placebo-controlled cross-over fashion. Metabolic rate, respiratory exchange ratio, and blood pressure were …

The Evolutionary History Of Cetacean Brain And Body Size, Stephen H. Montgomery, Jonathan H. Geisler, Michael R. Mcgowen, Charlotte Fox, Lori Marino, John Gatesy

Lori Marino, PhD

Cetaceans rival primates in brain size relative to body size and include species with the largest brains and biggest bodies to have ever evolved. Cetaceans are remarkably diverse, varying in both phenotypes by several orders of magnitude, with notable differences between the two extant suborders, Mysticeti and Odontoceti.We analyzed the evolutionary history of brain and body mass, and relative brain size measured by the encephalization quotient (EQ), using a data set of extinct and extant taxa to capture temporal variation in the mode and direction of evolution. Our results suggest that cetacean brain and body mass evolved under strong directional …

Orangutan Pantomime: Elaborating The Message, Anne Russon, Kristin Andrews

Kristin Andrews, PhD

We present an exploratory study of forest-living orangutan pantomiming, i.e. gesturing in which they act out their meaning, focusing on its occurrence, communicative functions, and complexities. Studies show that captive great apes may elaborate messages if communication fails, and isolated reports suggest that great apes occasionally pantomime. We predicted forest-living orangutans would pantomime spontaneously to communicate, especially to elaborate after communication failures. Mining existing databases on free-ranging rehabilitant orangutans’ behaviour identified 18 salient pantomimes. These pantomimes most often functioned as elaborations of failed requests, but also as deceptions and declaratives. Complexities identified include multimodality, re-enactments of past events and several …

The Production Of Biobutanol From Biomass Via A Hybrid Biological/Chemical Process, Thomas Melvin Potts

Graduate Theses and Dissertations

Biobutanol use as a fuel began in the late 19th century. Problems remain in economic viability. A review of the state of the art and need for technical advances is presented.

The technical potential of producing biofuel from a naturally occurring macroalgae was studied. The algae grow in Jamaica Bay, New York City, in contaminated water. The process consisted of mechanical harvesting, drying, grinding, and acid hydrolysis to form an algal sugar solution. Clostridium beijerinckii and C. saccharoperbutylacetonicum were used in an acetone butanol ethanol (ABE) fermentation to make butanol. Fermentation was followed by distillation Butanol concentrations during fermentation reached …

Structural And Functional Interactions Between Bro1 Domain Of Human Alix Protein And Nucleocapsid Packaging Rna Complex From Hiv, Scott Gross

Graduate School of Biomedical Sciences Theses and Dissertations

A virus is only as powerful as its ability to spread. Enveloped retroviruses, namely HIV-1, use exocytosis pathways that normal host cells use to release particles from the plasma membrane. The main pathways of interest in this study are the Endosomal Sorting Complex Required for Transport (ESCRT) and adjacent ALIX pathways. The ESCRT pathway is especially important for degradation of receptor/cargo complexes that form Multi-Vesicular Bodies (MVBs). Currently, there is no known therapy that targets this endosomal pathway, which would prevent the spread of the virus to other cells. The virus has adapted to jump from pathway to pathway when …

Characterization And Investigation Of Fungi Inhabiting The Gastrointestinal Tract Of Healthy And Diseased Humans, Mallory J. Suhr

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Gastrointestinal microbiome studies have failed to include fungi in total community analyses. As a result, their diversity and function in the gut is poorly understood. Recent work has begun to uncover the role intestinal fungi play in diet, immune system development, interactions with other microorganisms in the gut, and pathogenesis of diseases. Advances in sequencing technologies allow for the ability to profile the fungal gut microbiome (“mycobiome”) in healthy and diseased states. This thesis explores the mycobiome in 1) healthy humans with a vegetarian diet and 2) pediatric small bowel transplant recipients that develop fungal bloodstream infections.

The gut mycobiome …

Persister Cell Control Mechanisms In Uropathogenic Escherichia Coli, William H. Law Iii

Senior Honors Projects

Persister cells are a subpopulation of bacteria that demonstrate high tolerance to antibiotics, but revert to sensitivity after antibiotics are removed. The mechanism for induction of the persister cell state and antibiotic tolerance is not completely understood but likely occurs through the establishment of dormancy. Some of the suggested mechanisms for persister cell formation in Escherichia coli include: toxin­-antitoxin systems, starvation, gene regulation by (p)ppGpp, and stochastic formation. In our study we examine the mechanisms behind persistence in the E. coli strain CFT073, a uropathogenic isolate, which forms elevated levels of persisters compared to the laboratory strain MG1655. However, CFT073 …

Potential Role Of Rta3 And Gnp3 Transport Genes In The Quorum Sensing Response Of Candida Albicans, John G. Magnuson

Undergraduate Honors Theses

Quorum sensing (QS) is a mechanism of communication between cells to coordinate biological activities. In the opportunistic fungal pathogen Candida albicans, QS is important for regulating the organism’s ability to change morphology from a yeast form to a hyphal form. Previously, our laboratory identified several genes involved in polymicrobial communication between C. albicans and three bacterial species. We hypothesize that interspecies communication and QS utilize the same genetic pathways to control C. albicans morphological behavior. In this study, two transport genes, RTA3 and GNP3, and their involvement in QS were examined. To test whether these two genes participate in QS, …

Identification Of Transcription Factors Gzf3, Rfx1, Orf19.3928 As Being Implicated In Candida-Bacterial Interactions., Joni Watson

Undergraduate Honors Theses

Candida albicans is an opportunistic pathogen that is present in the normal flora in a majority of individuals. One key factor in C. albicans virulence is the ability to change its morphology from yeast to an elongated or hyphal form. The regulation of this morphogenesis relies in part upon quorum sensing (QS) molecules. C. albicans often exists as part of a mixed culture alongside other microbes and is influenced by their presence as well as the presence of QS molecules that they produce. In this study, a library of diploid homozygous transcriptional regulator knockout (TRKO) mutants were screened to identify …

Telling Stories Without Words, Kristin Andrews

Kristin Andrews, PhD

I will argue here that we can take a functional approach to FP that identifies it with the practice of explaining behaviour -- that is, we can understand folk psychology as having the purpose of explaining behaviour and promoting social cohesion by making others’ behaviour comprehensible, without thinking that this ability must be limited to those with linguistic abilities. One reason for thinking that language must be implicated in FP explanations arises from the history of theorizing about the nature of scientific explanation. I will show that there are other models of explanation that are free from the metaphysical linguistic …

Pantomime In Great Apes: Evidence And Implications, Ann E. Russon, Kristin Andrews

Kristin Andrews, PhD

We recently demonstrated, by mining observational data, that forest-living orangutans can communicate using gestures that qualify as Pantomime. Pantomimes, like other iconic gestures, physically resemble their referents. More elaborately, pantomimes involve enacting their referents. Holding thumb and finger together at the lips and blowing between them to mean balloon is one example. Here we sketch evidence of pantomime in other great apes, methodological concerns, and sophisticated cognitive capabilities that great ape pantomimes suggest.

Politics Or Metaphysics? On Attributing Psychological Properties To Animals, Kristin Andrews

Kristin Andrews, PhD

Following recent arguments that there is no logical problem with attributing mental or agential states to animals, I address the epistemological problem of how to go about making accurate attributions. I suggest that there is a two-part general method for determining whether a psychological property can be accurately attributed to a member of another species: folk expert opinion and functionality. This method is based on well-known assessments used to attribute mental states to humans who are unable to self-ascribe due to an early stage of development or impairment, and can be used to describe social and emotional development as well …

Are Apes’ Responses To Pointing Gestures Intentional?, Olivia Sultanescu, Kristin Andrews

Kristin Andrews, PhD

This paper examines the meaningfulness of pointing in great apes. We appeal to Hannah Ginsborg’s conception of primitive normativity, which provides an adequate criterion for establishing whether a response is meaningful, and we attempt to make room for a conception according to which there is no fundamental difference between the responses of human infants and those of other great apes to pointing gestures. This conception is an alternative to Tomasello’s view that pointing gestures and reactions to them reveal a fundamental difference between humans and other apes.

It's In Your Nature: A Pluralistic Folk Psychology, Kristin Andrews

Kristin Andrews, PhD

I suggest a pluralistic account of folk psychology according to which not all predictions or explanations rely on the attribution of mental states, and not all intentional actions are explained by mental states. This view of folk psychology is supported by research in developmental and social psychology. It is well known that people use personality traits to predict behavior. I argue that trait attribution is not shorthand for mental state attributions, since traits are not identical to beliefs or desires, and an understanding of belief or desire is not necessary for using trait attributions. In addition, we sometimes predict and …

Knowing Mental States: The Asymmetry Of Psychological Prediction And Explanation, Kristin Andrews

Kristin Andrews, PhD

Some interpretations of the two major theories of how minds understand minds, the theory theory and the simulation theory, conform to this require-ment of the Machiavellian intelligence thesis. Though both the theory theory and the simulation theory originated as accounts of how we understand other minds, it has been suggested that both simulation theory (e.g. Bolton 1995; Gordon 1995) and the theory theory (e.g. Frith and Happe 1999; Bolton 1995; Gopnick and Meltzoff 1994; Carruthers 1996) can also provide an account of how we understand our own minds. The classical account of how we know the contents of our own …

Cetaceans And Primates: Convergence In Intelligence And Self-Awareness, Lori Marino

Lori Marino, PhD

Cetaceans (dolphins, porpoises and whales) have been of greatest interest to the astrobiology community and to those interested in consciousness and selfawareness in animals. This interest has grown primarily from knowledge of the intelligence, language and large complex brains that many cetaceans possess. The study of cetacean and primate brain evolution and cognition can inform us about the contingencies and parameters associated with the evolution of complex intelligence in general, and, the evolution of consciousness. Striking differences in cortical organization in the brains of cetaceans and primates along with shared cognitive capacities such as self-awareness, culture, and symbolic concept comprehension, …

Do Zoos And Aquariums Promote Attitude Change In Visitors? A Critical Evaluation Of The American Zoo And Aquarium Study, Lori Marino, Scott O. Lilienfeld, Randy Malamud, Nathan Nobis, Ron Broglio

Lori Marino, PhD

Modern-day zoos and aquariums market themselves as places of education and conservation. A recent study conducted by the American Zoo and Aquarium Association (AZA) (Falk et al., 2007) is being widely heralded as the first direct evidence that visits to zoos and aquariums produce long-term positive effects on people’s attitudes toward other animals. In this paper, we address whether this conclusion is warranted by analyzing the study’s methodological soundness. We conclude that Falk et al. (2007) contains at least six major threats to methodological validity that undermine the authors’ conclusions. There remains no compelling evidence for the claim that zoos …

Towards A New Paradigm Of Non-Captive Research On Cetacean Cognition, Lori Marino, Toni Frohoff

Lori Marino, PhD

Contemporary knowledge of impressive neurophysiology and behavior in cetaceans, combined with increasing opportunities for studying free-ranging cetaceans who initiate sociable interaction with humans, are converging to highlight serious ethical considerations and emerging opportunities for a new era of progressive and less-invasive cetacean research. Most research on cetacean cognition has taken place in controlled captive settings, e.g., research labs, marine parks. While these environments afford a certain amount of experimental rigor and logistical control they are fraught with limitations in external validity, impose tremendous stress on the part of the captive animals, and place burdens on populations from which they are …