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Articles 1 - 30 of 568

Full-Text Articles in Life Sciences

The Effect Of Bacterial Endotoxin Lps On Serotonergic Modulation Of Glutamatergic Synaptic Transmission, Jate Bernard, Abigail Greenhalgh, Oscar Istas, Nicole T. Marguerite, Robin L. Cooper Aug 2020

The Effect Of Bacterial Endotoxin Lps On Serotonergic Modulation Of Glutamatergic Synaptic Transmission, Jate Bernard, Abigail Greenhalgh, Oscar Istas, Nicole T. Marguerite, Robin L. Cooper

Biology Faculty Publications

The release of the endotoxin lipopolysaccharides (LPS) from gram-negative bacteria is key in the induction of the downstream cytokine release from cells targeting cells throughout the body. However, LPS itself has direct effects on cellular activity and can alter synaptic transmission. Animals experiencing septicemia are generally in a critical state and are often treated with various pharmacological agents. Since antidepressants related to the serotonergic system have been shown to have a positive outcome for septicemic conditions impacting the central nervous system, the actions of serotonin (5-HT) on neurons also exposed to LPS were investigated. At the model glutamatergic synapse of ...


Exploration Of The Relationship Between The Fractal Dimension Of Microcalcification Clusters And The Hurst Exponent Of Background Tissue Disruption In Mammograms, Betelhem Abay Aug 2020

Exploration Of The Relationship Between The Fractal Dimension Of Microcalcification Clusters And The Hurst Exponent Of Background Tissue Disruption In Mammograms, Betelhem Abay

Honors College

Breast cancer is one of the most frequent cancers among women worldwide and holds the second place in cancer-related death. Mammography is the most commonly used screening technique, however, the dense nature of some breasts makes the analysis of mammograms challenging for radiologists. The 2D Wavelet Transform Modulus Maxima (WTMM) is one mathematical approach that is used to for the analysis of mammograms. In 2014, a team from the CompuMAINE Lab characterized differences between benign microcalcification clusters (MC) from malignant MC by calculating their fractal dimension, D, with the aid of the 2D WTMM method. In a different implementation of ...


Study Of Pharmaceutical Tablets Using Raman Mapping, Kyle Joseph Pauly May 2020

Study Of Pharmaceutical Tablets Using Raman Mapping, Kyle Joseph Pauly

Honors Theses

Covalent bonds are the strongest type of bonds holding molecules together. Based on the pattern of bonding of the molecule, the atoms associated with the bond will vibrate at a specific frequency. Utilizing vibrational spectroscopy, such as Raman spectroscopy, these unique vibrational frequencies can be used to detect the presence of analytes over a selected area. Furthermore, the intensities of the vibrational modes can be tracked to comparatively quantify the concentration of analytes at various locations. This is a method of great importance due to its ability to compare pharmaceutical tablets synthesized with different techniques. Here, the presence and concentration ...


Integrating The Ecosystem Services Framework To Define Dysbiosis Of The Breastfed Infant Gut: The Role Of B. Infantis And Human Milk Oligosaccharides, Rebbeca M. Duar, Bethany M. Henrick, Giorgio Casaburi, Steven A. Frese Apr 2020

Integrating The Ecosystem Services Framework To Define Dysbiosis Of The Breastfed Infant Gut: The Role Of B. Infantis And Human Milk Oligosaccharides, Rebbeca M. Duar, Bethany M. Henrick, Giorgio Casaburi, Steven A. Frese

Faculty Publications in Food Science and Technology

Mounting evidence supports a connection between the composition of the infant gut microbiome and long-term health. In fact, aberrant microbiome compositions during key developmental windows in early life are associated with increased disease risk; therefore, making pertinent modifications to the microbiome during infancy offers significant promise to improve human health. There is growing support for integrating the concept of ecosystem services (the provision of benefits from ecosystems to humans) in linking specific microbiome functions to human well-being. This framework is widely applied in conservation efforts of macro-ecosystems and offers a systematic approach to guide restoration actions aimed to recover critical ...


Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone Feb 2020

Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

Biology Faculty Articles

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors ...


Biogeographic Study Of Human Gut-Associated Crassphage Suggests Impacts From Industrialization And Recent Expansion, Tanvi P/ Honap, Krithivasan Sankaranarayanan, Stephanie L. Schnorr, Andrew T. Ozga, Christina Warinner, Cecil M. Lewis Jr. Jan 2020

Biogeographic Study Of Human Gut-Associated Crassphage Suggests Impacts From Industrialization And Recent Expansion, Tanvi P/ Honap, Krithivasan Sankaranarayanan, Stephanie L. Schnorr, Andrew T. Ozga, Christina Warinner, Cecil M. Lewis Jr.

Anthropology Faculty Publications

CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as ...


Toward A Neurological Understanding Of Metacognition, Philip Hulbig Jan 2020

Toward A Neurological Understanding Of Metacognition, Philip Hulbig

Educational Studies Dissertations

Metacognitive interventions have been shown to be tremendously important to general education and supporting individuals with neurological disabilities (Brown, 1978; Webb, 1989; Dunlosky & Metcalfe, 2009; Dweck, 2017). This paper details the many facets and relationships between neurology and metacognition. The investigation draws from a wide diversity of neuro-investigational techniques and findings related to metacognition, executive function, self-reflection, self-evaluation, self-development and self-directed learning. It ends with a discussion of common threads and themes drawn from the research, and how methodological definitions for metacognitive knowledge and metacognitive regulation can be combined with physiologically-focused neurobiological approaches and consciousness-focused psychological approaches to broaden understanding and further ...


A Potential Role Of Evolution In Shaping Modern Human's Behaviors And Morals, Madeleine Sarner Jan 2020

A Potential Role Of Evolution In Shaping Modern Human's Behaviors And Morals, Madeleine Sarner

Honors Theses

Between eight and six million years ago there existed a common ancestor linking the human species with their great ape relatives. Following the arrival of this organism, a lineage of several different human species began to emerge around two to three million years ago in Africa. These species included Homo rudolfensis, Homo habilis, Homo ergaster, Homo erectus, Homo floresiensis, Homo heidelbergensis, Homo neanderthalensis, and Homo sapiens. By analyzing these species and the great ape relatives through literary research, it is possible to begin to investigate the potential role of evolution in constructing modern human behaviors and morals.


A Flight Sensory-Motor To Olfactory Histamine Circuit Mediates Olfactory Processing Of Ecologically And Behaviorally Natural Stimuli, Samual P. Bradley Jan 2020

A Flight Sensory-Motor To Olfactory Histamine Circuit Mediates Olfactory Processing Of Ecologically And Behaviorally Natural Stimuli, Samual P. Bradley

Graduate Theses, Dissertations, and Problem Reports

Environmental pressures have conferred species specific behavioral and morphological traits to optimize reproductive success. To optimally interact with their environment, nervous systems have evolved motor-to-sensory circuits that mediate the processing of its own reafference. Moth flight behavioral patterns to odor sources are stereotyped, presumably to optimize the likelihood of interacting with the odor source. In the moth Manduca sexta wing beating causes oscillatory flow of air over the antenna; because of this, odorant-antennal interactions are oscillatory in nature. Electroantennogram recordings on antennae show that the biophysical properties of their spiking activity can effectively track odors presented at the wing beat ...


Of Elephants And Men, Helen Kopnina Jan 2020

Of Elephants And Men, Helen Kopnina

Animal Sentience

Baker & Winkler’s target article is well-researched and thought-provoking, but I do have four points of contention: (1) The proposal to entrust elephants to traditional mahout culture has restricted elephants’ freedom of movement and reproduction and (ab)used them. (2) The concept of “indigenous” simultaneously reifies and denigrates the “noble savages”, privileging only human indigenous groups, ignoring nonhuman indigenes. (3) Most lifestyles have been globalized under consumer-economic and anthropocentric worldviews. (4) The fact that people (including mahouts) are part of nature does not mean they are benevolent, any more than cities, monocultures, or roads are.


Rewilding And Domestication: Clarifying Terminology, Catia Correia-Caeiro Jan 2020

Rewilding And Domestication: Clarifying Terminology, Catia Correia-Caeiro

Animal Sentience

Baker & Winkler (B&W) describe the state of Asian elephant conservation, raising unique issues, and proposing a direction based on rewilding. The long history and socio-biology of elephants and humans has some parallels with the domestication of dogs (and other species). However, markers of domestication seem absent from elephants. The proper use of terms such as “wild” and “domestic” is crucial in defining the best conservation strategies, and, more important, in attending to the welfare needs of individuals, which can differ between wild and domestic animals. B&W’s target article represents an important starting point for discussion around elephant ...


Oral Microbiome Diversity In Chimpanzees From Gombe National Park, Andrew T. Ozga, Ian C. Gilby, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Anne C. Stone Nov 2019

Oral Microbiome Diversity In Chimpanzees From Gombe National Park, Andrew T. Ozga, Ian C. Gilby, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Anne C. Stone

Biology Faculty Articles

Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome ...


How Do Humans Process Magnitudes? An Examination Of The Neural And Cognitive Underpinnings Of Symbols, Quantities, And Size In Adults And Children, Helen Moriah Sokolowski Oct 2019

How Do Humans Process Magnitudes? An Examination Of The Neural And Cognitive Underpinnings Of Symbols, Quantities, And Size In Adults And Children, Helen Moriah Sokolowski

Electronic Thesis and Dissertation Repository

A striking way that humans differ from other species is our unique ability to represent and manipulate symbols. This ability to process numerical magnitudes symbolically (e.g., ‘three’, ‘3’) is widely thought to be supported by an ancient system that evolved to process nonsymbolic numerical magnitudes (i.e., quantities). In this thesis, I present four empirical studies to uncover whether symbolic representations are indeed supported by the system that evolved to process quantities, or if symbolic representations are sub-served by a similar but ultimately distinct system.

In experiments 1 and 2, I investigate how the adult brain processes symbols and ...


How Does The Brain Represent Digits? Investigating The Neural Correlates Of Symbolic Number Representation Using Fmri-Adaptation, Celia Goffin Oct 2019

How Does The Brain Represent Digits? Investigating The Neural Correlates Of Symbolic Number Representation Using Fmri-Adaptation, Celia Goffin

Electronic Thesis and Dissertation Repository

How does the brain represent numerical symbols (e.g., Arabic digits)? Activity in left parietal regions correlates with symbolic number processing. Research with functional resonance imaging adaptation (fMRI-A) indicates that the intraparietal sulcus (IPS) exhibits a rebound (increase in activation) effect when a repeatedly presented number is followed by a new number. Importantly, this rebound effect is modulated by numerical ratio as well as the difference between presented numbers (distance). This ratio-dependent rebound effect could reflect a link between symbolic numerical representation and an approximate number system (ANS). In this doctoral dissertation, fMRI-A is used to investigate mechanisms underlying symbolic ...


Tooth Fracture Frequency In Gray Wolves Reflects Prey Availability., Blaire Van Valkenburgh, Rolf O. Peterson, Douglas W Smith, Daniel R Stahler, John A. Vucetich Sep 2019

Tooth Fracture Frequency In Gray Wolves Reflects Prey Availability., Blaire Van Valkenburgh, Rolf O. Peterson, Douglas W Smith, Daniel R Stahler, John A. Vucetich

Michigan Tech Publications

Exceptionally high rates of tooth fracture in large Pleistocene carnivorans imply intensified interspecific competition, given that tooth fracture rises with increased bone consumption, a behavior that likely occurs when prey are difficult to acquire. To assess the link between prey availability and dental attrition, we documented dental fracture rates over decades among three well-studied populations of extant gray wolves that differed in prey:predator ratio and levels of carcass utilization. When prey:predator ratios declined, kills were more fully consumed, and rates of tooth fracture more than doubled. This supports tooth fracture frequency as a relative measure of the difficulty ...


Thinking About Thinking Chickens, Lori Marino Sep 2019

Thinking About Thinking Chickens, Lori Marino

Lori Marino, PhD

This response focuses on three major conceptual threads that run through the peer commentary on my target article: (1) how the use of chickens influences our views of them, (2) whether education is effective, and (3) what components of chicken psychology are most relevant to understanding who chickens are.



The Inconvenient Truth About Thinking Chickens, Lori Marino Sep 2019

The Inconvenient Truth About Thinking Chickens, Lori Marino

Lori Marino, PhD

Original Abstract: Domestic chickens are members of an order, Aves, which has been the focus of a revolution in our understanding of neuroanatomical, cognitive, and social complexity. Some birds are now known to be on a par with many mammals in their intelligence, emotional sophistication, and social interaction. Yet views of chickens have largely remained unrevised in light of this new evidence. In this paper, I examine the data on cognition, emotions, personality, and sociality in chickens, exploring such areas as self-awareness, cognitive bias, social learning and self-control, and comparing their abilities with other birds and other vertebrates, particularly mammals ...


Intelligence, Complexity, And Individuality In Sheep, Lori Marino, Debra Merskin Sep 2019

Intelligence, Complexity, And Individuality In Sheep, Lori Marino, Debra Merskin

Lori Marino, PhD

Domestic sheep (Ovis aries) are among the earliest animals domesticated for human use. They are consumed worldwide as mutton, hogget, and lamb, kept as wool and milk producers, and used extensively in scientific research. The popular stereotype is that sheep are docile, passive, unintelligent, and timid, but a review of the research on their behavior, affect, cognition, and personality reveals that they are complex, individualistic, and social.


The State Of The Animals Iii: 2005, Deborah J. Salem, Andrew N. Rowan Sep 2019

The State Of The Animals Iii: 2005, Deborah J. Salem, Andrew N. Rowan

Andrew N. Rowan, DPhil

In this third, all new, volume in the State of the Animals series, scholars and experts in animal protection examine the challenges facing companion animals, marine mammals, and nonhuman primates and review legal protection for animals here and abroad.


The Animal Research Controversy: Protest, Process & Public Policy, Andrew N. Rowan, Franklin M. Loew, Joan C. Weer Sep 2019

The Animal Research Controversy: Protest, Process & Public Policy, Andrew N. Rowan, Franklin M. Loew, Joan C. Weer

Andrew N. Rowan, DPhil

The controversy today regarding the use of animals in research appears on the surface to be a strongly polarized struggle between the scientific community and the animal protection movement. However, there is a wide range of opinions and philosophies on both sides. Mistrust between the factions has blossomed while communication has withered. Through the 1960s, 1970s and early 1980s, the animal movement grew in numbers and financial resources, and developed much greater public recognition and political clout. The research community paid relatively little attention to the animal movement for much of this period but, alarmed by several public relations coups ...


Innate Antibodies, Murine Models, And Evolution: A Study Of Trypanosome Lytic Factor Functions And Their Translational Applications, Joseph P. Verdi Sep 2019

Innate Antibodies, Murine Models, And Evolution: A Study Of Trypanosome Lytic Factor Functions And Their Translational Applications, Joseph P. Verdi

Dissertations, Theses, and Capstone Projects

Trypanosome lytic factors (TLFs) are primate-specific antimicrobial protein complexes that lyse African trypanosome parasites by delivering the channel-forming toxin APOL1 to the invading microorganisms. Human serum contains two TLFs that are delivered to the parasite by separate mechanisms, only one of which has been characterized. TLF1 is endocytosed by a receptor that is typically blocked by other serum factors in vivo, suggesting that TLF2 is the more relevant lytic factor in the context of trypanosome immunity. TLF2 is non-covalently associated with polyclonal immunoglobulin M (IgM) antibodies, which we report here to be involved in the uptake mechanism. The TLF2-IgMs are ...


Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr. Aug 2019

Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr.

Andrew Ozga

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26 ...


Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner Aug 2019

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Andrew Ozga

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon ...


Progressive Alignment With Cactus: A Multiple-Genome Aligner For The Thousand-Genome Era, Joel Armstrong, Elinor K. Karlsson, Benedict Paten Aug 2019

Progressive Alignment With Cactus: A Multiple-Genome Aligner For The Thousand-Genome Era, Joel Armstrong, Elinor K. Karlsson, Benedict Paten

University of Massachusetts Medical School Faculty Publications

Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology ...


The Genesis Of Malaria: The Origin Of Mosquitoes And Their Protistan Cargo, Plasmodium Falciparum, Alan L. Gillen, Frank Sherwin Jul 2019

The Genesis Of Malaria: The Origin Of Mosquitoes And Their Protistan Cargo, Plasmodium Falciparum, Alan L. Gillen, Frank Sherwin

Alan L. Gillen

Malaria is caused by the parasite belonging to the genus Plasmodium; however, creation biologists maintain this organism was not always parasitic. Plasmodium is probably a degenerate form of algae. Mosquitoes, the vector of Plasmodium, were probably designed to be pollinators, not parasite vectors. In this article, we present both the evolutionary and creation explanation for the origin of malaria with a mention to its vector, the mosquito.

The purpose of this article is to provide a reasonable explanation for the genesis of malaria. Microbiology and parasitology research based on the creation paradigm appears to provide some answers to these puzzling ...


Taxonomic Features And Comparison Of The Gut Microbiome From Two Edible Fungus-Farming Termites (Macrotermes Falciger, M. Natalensis) Harvested In The Vhembe District Of Limpopo, South Africa, Stephanie L. Schnorr, Courney A. Hofman, Shandukani R. Netschifhefhe, Frances D. Duncan, Tanvi P. Honap, Julie Lesnik, Cecil M. Lewis Jul 2019

Taxonomic Features And Comparison Of The Gut Microbiome From Two Edible Fungus-Farming Termites (Macrotermes Falciger, M. Natalensis) Harvested In The Vhembe District Of Limpopo, South Africa, Stephanie L. Schnorr, Courney A. Hofman, Shandukani R. Netschifhefhe, Frances D. Duncan, Tanvi P. Honap, Julie Lesnik, Cecil M. Lewis

Anthropology Faculty Publications

Background Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming ‘higher’ termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of edible termites is well known, their microbiomes are unexplored in the context of human health. Here we sequenced the V4 region of the 16S rRNA gene of gut microbiota extracted from the whole intestinal tract of two Macrotermes sp. soldiers collected from the Limpopo region of South Africa. Results ...


Critically Evaluating Animal Research, Andrew Knight Jul 2019

Critically Evaluating Animal Research, Andrew Knight

Andrew Knight, PhD

No abstract provided.


Probability, Populations, Phylogenetics And Hominin Speciation, Niccolo Caldararo Jul 2019

Probability, Populations, Phylogenetics And Hominin Speciation, Niccolo Caldararo

Human Biology Open Access Pre-Prints

A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mtDNA sequences from the fossil remains of a number of Neandertal fossils and the Denisovans in an attempt to understand the evolution of Mid Pleistocene human ancestors. These papers, introduce a number of problems in the interpretation of speciation in hominins. One concerns the degradation of the ancient DNA and its interpretation as authentic genetic information. Another concerns the idea of “species” versus that of “population” and the use of ...


Paired-End Mappability Of Transposable Elements In The Human Genome, Corinne E. Sexton, Mira V. Han Jul 2019

Paired-End Mappability Of Transposable Elements In The Human Genome, Corinne E. Sexton, Mira V. Han

Life Sciences Faculty Publications

Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely ...


Orca Behavior And Subsequent Aggression Associated With Oceanarium Confinement, Robert Anderson, Robyn Waayers, Andrew Knight Jul 2019

Orca Behavior And Subsequent Aggression Associated With Oceanarium Confinement, Robert Anderson, Robyn Waayers, Andrew Knight

Andrew Knight, PhD

Based on neuroanatomical indices such as brain size and encephalization quotient, orcas are among the most intelligent animals on Earth. They display a range of complex behaviors indicative of social intelligence, but these are difficult to study in the open ocean where protective laws may apply, or in captivity, where access is constrained for commercial and safety reasons. From 1979 to 1980, however, we were able to interact with juvenile orcas in an unstructured way at San Diego’s SeaWorld facility. We observed in the animals what appeared to be pranks, tests of trust, limited use of tactical deception, emotional ...