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Articles 1 - 26 of 26
Full-Text Articles in Life Sciences
Ultracontinuous Single Haplotype Genome Assemblies For The Domestic Cat (Felis Catus) And Asian Leopard Cat (Prionailurus Bengalensis), Kevin R. Bredemeyer, Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody E. Roelke-Parker, Stephen James O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
Ultracontinuous Single Haplotype Genome Assemblies For The Domestic Cat (Felis Catus) And Asian Leopard Cat (Prionailurus Bengalensis), Kevin R. Bredemeyer, Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody E. Roelke-Parker, Stephen James O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
Biology Faculty Articles
In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the …
Antimicrobial Peptide Development: From Massively Parallel Peptide Sequencing To Bioinformatic Motif Identification, Alexander K. Erikson
Antimicrobial Peptide Development: From Massively Parallel Peptide Sequencing To Bioinformatic Motif Identification, Alexander K. Erikson
Theses and Dissertations
The isolation, purification, and clinical deployment of antibiotics is one of the major drivers of decrease in morbidity and mortality from infectious bacteria in the 20th century. The rapid, ubiquitous deployment of antibiotics encouraged swift development and distribution of antibiotic resistance. New, novel techniques, technologies, and ultimately therapeutic antimicrobial compounds will be required to counter the rise of antibiotic resistant microbes. Historically, mimicking naturally occurring compounds has been the most fruitful method for discovering new antibiotics; unsurprisingly, many recent efforts have focused on expanding the cultivation and detection of previously unknown microbes and compounds, respectively. Other techniques explore developing compounds …
Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso
Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso
University of New Orleans Theses and Dissertations
One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …
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
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 …
Porcine Cytokines, Chemokines And Growth Factors: 2019 Update, Harry D. Dawson, Yongming Sang, Joan K. Lunney
Porcine Cytokines, Chemokines And Growth Factors: 2019 Update, Harry D. Dawson, Yongming Sang, Joan K. Lunney
Agricultural and Environmental Sciences Faculty Research
Pigs are a major food source worldwide as well as major biomedical models for human physiology and therapeutics. A thorough understanding of porcine immunity is essential to prevent and treat infectious diseases, and develop effective vaccines and therapeutics. The use of pigs as biomedical models is dependent on the growing molecular and immune toolbox. This paper summarizes current knowledge of swine cytokines, chemokines and growth factors, identifying 289 pig proteins, characterizing knowledge of their gene structures and families. It identifies areas in the current swine genome build that need to be clarified. A broad-based literature and vendor search was conducted …
Multiple Fgf4 Retrocopies Recently Derived Within Canids, Kevin Batcher, Peter Dickinson, Kimberly Maciejczyk, Kristin Brzeski, Sheida Hadji Rasouliha, Anna Letko, Cord Drögemüller, Tosso Leeb, Danika Bannasch
Multiple Fgf4 Retrocopies Recently Derived Within Canids, Kevin Batcher, Peter Dickinson, Kimberly Maciejczyk, Kristin Brzeski, Sheida Hadji Rasouliha, Anna Letko, Cord Drögemüller, Tosso Leeb, Danika Bannasch
Michigan Tech Publications
Two transcribed retrocopies of the fibroblast growth factor 4 (FGF4) gene have previously been described in the domestic dog. An FGF4 retrocopy on chr18 is associated with disproportionate dwarfism, while an FGF4 retrocopy on chr12 is associated with both disproportionate dwarfism and intervertebral disc disease (IVDD). In this study, whole-genome sequencing data were queried to identify other FGF4 retrocopies that could be contributing to phenotypic diversity in canids. Additionally, dogs with surgically confirmed IVDD were assayed for novel FGF4 retrocopies. Five additional and distinct FGF4 retrocopies were identified in canids including a copy unique to red wolves (Canis rufus). The …
Plasmodium Impairs Antibacterial Innate Immunity To Systemic Infections In Part Through Hemozoin-Bound Bioactive Molecules., Christopher Lynn Harding
Plasmodium Impairs Antibacterial Innate Immunity To Systemic Infections In Part Through Hemozoin-Bound Bioactive Molecules., Christopher Lynn Harding
Electronic Theses and Dissertations
Despite efforts to decrease the global health burden of malaria, infections with Plasmodium species continue to cause over 200 million episodes of malaria each year which resulted in 405,000 deaths in 2018 [1]. One complication of malaria is increased susceptibility to invasive bacterial infections. Plasmodium infections impair host immunity to non-Typhoid Salmonella (NTS) through activities of heme oxygenase I (HO-I) )-induced release of immature granulocytes and myeloid cell-derived IL-10. Yet, it is not known if these mechanisms are specific to NTS. We show here, that Plasmodium yoelii 17XNL (Py) infected mice had impaired clearance of systemic Listeria monocytogenes (Lm) during …
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 …
Brain Micrornas Among Social And Solitary Bees, Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben-Shahar
Brain Micrornas Among Social And Solitary Bees, Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben-Shahar
Biology Faculty Publications
Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20–35%) of detected miRNAs had lineage-specific expression in the brain, 24–72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression …
Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa
Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa
Electronic Thesis and Dissertation Repository
In the field of bioinformatics, taxonomic classification is the scientific practice of identifying, naming, and grouping of organisms based on their similarities and differences. The problem of taxonomic classification is of immense importance considering that nearly 86% of existing species on Earth and 91% of marine species remain unclassified. Due to the magnitude of the datasets, the need exists for an approach and software tool that is scalable enough to handle large datasets and can be used for rapid sequence comparison and analysis. We propose ML-DSP, a stand-alone alignment-free software tool that uses Machine Learning and Digital Signal Processing to …
Snapshots Of Human Anatomy, Locomotion, And Behavior From Late Pleistocene Footprints At Engare Sero, Tanzania, Kevin Hatala, William E. H. Harcourt-Smith, Adam D. Gordon, Brian W. Zimmer, Brian G. Richmond, Briana L. Pobiner, David J. Green, Adam Metallo, Vince Rossi, Cynthia M. Liutkus-Pierce
Snapshots Of Human Anatomy, Locomotion, And Behavior From Late Pleistocene Footprints At Engare Sero, Tanzania, Kevin Hatala, William E. H. Harcourt-Smith, Adam D. Gordon, Brian W. Zimmer, Brian G. Richmond, Briana L. Pobiner, David J. Green, Adam Metallo, Vince Rossi, Cynthia M. Liutkus-Pierce
Publications and Research
Fossil hominin footprints preserve data on a remarkably short time scale compared to most other fossil evidence, offering snapshots of organisms in their immediate ecological and behavioral contexts. Here, we report on our excavations and analyses of more than 400 Late Pleistocene human footprints from Engare Sero, Tanzania. The site represents the largest assemblage of footprints currently known from the human fossil record in Africa. Speed estimates show that the trackways reflect both walking and running behaviors. Estimates of group composition suggest that these footprints were made by a mixed-sex and mixed-age group, but one that consisted of mostly adult …
Study Of Pharmaceutical Tablets Using Raman Mapping, Kyle Joseph Pauly
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 …
Novel Method To Determine Paleodiet Of Extinct Equid Merychippus Sp. Using Dental Calculus, Ranjit Z. S. Virk
Novel Method To Determine Paleodiet Of Extinct Equid Merychippus Sp. Using Dental Calculus, Ranjit Z. S. Virk
Senior Honors Projects, 2020-current
Within the Miocene Epoch, the emergence of grasslands within North America coincided with the incidence of higher-crowned teeth (hypsodonty) within the proto-horse Merychippus that allowed for the inclusion of these expanding grasslands as a food source. As herbivorous paleofauna consume plant matter, microscopic remains become incorporated within dental calculus and, due to their diagnostic morphology, can be used to identify dietary components. In Merychippus, the recovery of plant microfossils holds the potential to provide greater clarity on the paleodiet of these equids. In the present study, the purpose was to quantify and compare Merychippus paleodiet constituents among sample groups. …
Ontogenetic And Adult Shape Variation In The Endocast Of Tapirus: Implications For T. Polkensis From The Gray Fossil Site, Thomas M. Gaetano
Ontogenetic And Adult Shape Variation In The Endocast Of Tapirus: Implications For T. Polkensis From The Gray Fossil Site, Thomas M. Gaetano
Electronic Theses and Dissertations
Endocranial morphology provides evidence of sensory ecology and sociality of extinct vertebrates. The Earliest Pliocene Gray Fossil Site (GFS) of NE Tennessee features a conspicuous dominance of skeletal elements belonging to the dwarf tapir, Tapirus polkensis. Numerous individuals in one fossil locality often suggests gregarious behavior, but sociality in T. polkensis contradicts behavior documented for extant Tapirus species. I test T. polkensis for variation in sensory and social ecology using computed tomography and 3D digital endocasts from an ontogenetic sequence. I compare the T. polkensis endocasts with extant Tapirus species using Encephalization Quotients (EQs) and 3D geometric morphometrics. Results …
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
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
Department of Food Science and Technology: Faculty Publications
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 …
Evolutionary Traits That Enable Scleractinian Corals To Survive Mass Extinction Events, Gal Dishon, Michal Grossowicz, Michael Krom, Gilad Guy, David F. Gruber, Dan Tchernov
Evolutionary Traits That Enable Scleractinian Corals To Survive Mass Extinction Events, Gal Dishon, Michal Grossowicz, Michael Krom, Gilad Guy, David F. Gruber, Dan Tchernov
Publications and Research
Scleractinian “stony” corals are major habitat engineers, whose skeletons form the framework for the highly diverse, yet increasingly threatened, coral reef ecosystem. Fossil coral skeletons also present a rich record that enables paleontological analysis of coral origins, tracing them back to the Triassic (~241 Myr). While numerous invertebrate lineages were eradicated at the last major mass extinction boundary, the Cretaceous-Tertiary/K-T (66 Myr), a number of Scleractinian corals survived. We review this history and assess traits correlated with K-T mass extinction survival. Disaster-related “survival” traits that emerged from our analysis are: (1) deep water residing (>100 m); (2) cosmopolitan distributions, …
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
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 …
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.
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 Research
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 compared to …
Rewilding And Domestication: Clarifying Terminology, Catia Correia-Caeiro
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 conservation, but …
Investigation On The Human Coronaviruses Origin (Bats And Pangolins): A Review, James Blackar Mawolo, Caselia Akiti, Harris Kollie Momo
Investigation On The Human Coronaviruses Origin (Bats And Pangolins): A Review, James Blackar Mawolo, Caselia Akiti, Harris Kollie Momo
Turkish Journal of Zoology
A coronavirus related to SARS-CoV-2 has been isolated from Malayan pangolins illegally imported into Guangdong Province. It is not the precursor of SARS-CoV-2, but a comparison of viral genome sequences provides further evidence that the virus currently infecting humans. Bats and pangolins have been suggested as the natural reservoirs of a large variety of viruses. Some researchers have given attention to other species as the origin of coronaviruses and none have referred to bats and pangolins as the two emerging coronaviruses origin, which have caused unexpected human disease outbreaks recently. Severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East …
Affective Sentience And Moral Protection, Russell Powell, Irina Mikhalevich
Affective Sentience And Moral Protection, Russell Powell, Irina Mikhalevich
Animal Sentience
We have structured our response according to five questions arising from the commentaries: (i) What is sentience? (ii) Is sentience a necessary or sufficient condition for moral standing? (iii) What methods should guide comparative cognitive research in general, and specifically in studying invertebrates? (iv) How should we balance scientific uncertainty and moral risk? (v) What practical strategies can help reduce biases and morally dismissive attitudes toward invertebrates?
Of Elephants And Men, Helen Kopnina
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.
Profiling Transcription And Retrotransposition Of Mouse L1 Subfamilies, Lingqi Kong
Profiling Transcription And Retrotransposition Of Mouse L1 Subfamilies, Lingqi Kong
Electronic Theses and Dissertations
Transposable elements, also called jumping genes, comprise almost 45% of the human genome. In contrast, only 1% of the human genome is protein-coding sequences. The function and advantages of maintaining such massive copies of transposable elements in the human genome are still unclear. Long interspersed element 1 (L1), the most substantial group and the only active autonomous transposable element in the human genome, has revealed its unique roles in many diseases. The insertional mutagenesis induced by L1 retrotransposition events could threaten human genomic stability and generate unexpected mutations. L1 overexpression has been documented in both somatic and germline cells and, …
Gut Microbiota Composition Is Correlated To Host Hummingbird Protein Requirements, Ryan C. Stanton , '20
Gut Microbiota Composition Is Correlated To Host Hummingbird Protein Requirements, Ryan C. Stanton , '20
Senior Theses, Projects, and Awards
The gut microbiome shapes and is shaped by a host animal’s physiology. Avian taxa hold physiological characteristics unique from mammals and might inform novel pressures experienced by microbial communities. Further, the symbionts’ relative abundance and their abilities to adapt to available resources are of critical importance to a holobiont’s fitness in rapidly changing climates. Therefore, wild populations of hummingbirds Selasphorus rufus and Calypte anna were studied. The two systems differ in S. rufus’s annual migrations from wintering grounds to their breeding grounds in the Pacific Northwest, whereas C. anna are resident in the latter region. Previous findings have indicated …
A Flight Sensory-Motor To Olfactory Histamine Circuit Mediates Olfactory Processing Of Ecologically And Behaviorally Natural Stimuli, Samual P. Bradley
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 …
A Potential Role Of Evolution In Shaping Modern Human's Behaviors And Morals, Madeleine Sarner
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.