Life Sciences Commons^™

Expression And Role Of Gonadotropin-Releasing Hormone 2 And Its Receptor In Mammals, Amy Desaulniers, Rebecca A. Cederberg, Clay A. Lents, Brett R. White

Department of Animal Science: Faculty Publications

Gonadotropin-releasing hormone 1 (GnRH1) and its receptor (GnRHR1) drive mammalian reproduction via regulation of the gonadotropins. Yet, a second form of GnRH (GnRH2) and its receptor (GnRHR2) also exist in mammals. GnRH2 has been completely conserved throughout 500 million years of evolution, signifying high selection pressure and a critical biological role. However, the GnRH2 gene is absent (e.g., rat) or inactivated (e.g., cow and sheep) in some species but retained in others (e.g., human, horse, and pig). Likewise, many species (e.g., human, chimpanzee, cow, and sheep) retain the GnRHR2 gene but lack the appropriate coding sequence to produce a full-length …

The Role Of Isolation On Contrasting Phylogeographic Patterns In Two Cave Crustaceans, Jorge L. Pérez-Moreno, Gergely Balázs, Blake Wilkins, Gábor Herczeg, Heather D. Bracken-Grissom

Center for Coastal Oceans Research Faculty Publications

Background:

The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution. The present project aims to examine the phylogeographic patterns exhibited by two sympatric species of surface and cave-dwelling peracarid crustaceans (Asellus aquaticus and Niphargus hrabei), and in doing so elucidate the possible roles …

Why Are We Compelled To Do Science? (Participant's Guide), Lydia Marcus

Study Guides for Faith & Science Integration

A study of The Penultimate Curiosity: How Science Swims in the Sliptream of Ultimate Questions

Why Are We Compelled To Do Science? (Leader's Guide), Lydia Marcus

Study Guides for Faith & Science Integration

A Study of The Penultimate Curiosity: How Science Swims in the Slipstream of Ultimate Questions

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Catherine Putonti

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …

The Inconvenient Truth About Thinking Chickens, Lori Marino

Animal Sentience

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 …

Infectious Disease And The Diversification Of The Human Genome, Jessica F. Brinkworth

Human Biology Open Access Pre-Prints

The human immune system is under great pathogen-mediated selective pressure. A combination of divergent infectious disease pathogenesis across human populations, and the overrepresentation of “immune genes” in genomic regions with signatures of positive selection suggests that pathogens have significantly altered the human genome. However, important features of the human immune system can confound searches for and interpretations of signatures of pathogen-mediated evolution. Immune system redundancy, immune gene pleiotropy, host ability to acquire immunity and alter the immune repertoire of their offspring through “priming”, and host microbiome complicate evolutionary interpretations of host- pathogen interactions. The overall promiscuity and sensitivity of the …

Trypanosome Lytic Factor Mediated Immunity Against Leishmania Sp., Jyoti Pant

Dissertations, Theses, and Capstone Projects

Trypanosome Lytic Factor (TLF) is an innate immunity complex that was originally discovered to protect against African Trypanosomes. The major components of TLF are Apolipoprotein A1 (APOA1), Apolipoprotein L1 (APOL1) and HPR (Haptoglobin Related Protein), where APOL1 is necessary and sufficient for trypanolysis. Recently we have shown that TLF ameliorates infections by cutaneous Leishmania species. Here we investigated the effect of different primate and human TLF against different Leishmania sp. Our result shows that TLF kills metacyclic promastigotes of cutaneous Leishmania sp. within immune cells such as neutrophils and macrophages by two different mechanism. Using transiently transfected and germline transgenic …

Unravelling Organelle Genome Transcription Using Publicly Available Rna-Sequencing Data, Matheus Sanita Lima

Electronic Thesis and Dissertation Repository

The study of organelles helped forge theories of genome evolution because of their unconventional genomes and gene expression regimes. The organelle genomics field (~35 years old) has seen the development of next generation sequencing (NGS) techniques and the consequent skyrocketing of genomic and transcriptomic data. However, these data are being underused in the studies of organelle genome transcription. My thesis investigates how NGS has affected the field of organelle genomics at both the DNA and RNA levels. First, I demonstrate that although organelle genomes are being sequenced as never before, they are un-characterized as they are published mostly as “organelle …

Across The Indian Ocean: A Remarkable Example Of Trans-Oceanic Dispersal In An Austral Mygalomorph Spider, Sophie E. Harrison, Mark S. Harvey, Steve J.B. Cooper, Andrew D. Austin, Michael G. Rix

Research outputs 2014 to 2021

The Migidae are a family of austral trapdoor spiders known to show a highly restricted and disjunct distribution pattern. Here, we aim to investigate the phylogeny and historical biogeography of the group, which was previously thought to be vicariant in origin, and examine the biogeographic origins of the genus Moggridgea using a dated multi-gene phylogeny. Moggridgea specimens were sampled from southern Australia and Africa, and Bertmainus was sampled from Western Australia. Sanger sequencing methods were used to generate a robust six marker molecular dataset consisting of the nuclear genes 18S rRNA, 28S rRNA, ITS rRNA, XPNPEP3 and H3 and the …

Assessing The Sustainability Of Waiwai Subsistence Hunting In Guyana With Implications For Co-Management In Amazonian Indigenous Reserves, Christopher Shaffer, Charakura Yukuma, Elisha Marawanaru, Phillip Suse

Funded Articles

While bushmeat hunting is critical to the livelihoods of millions of people throughout the tropical world, it is also a major threat to wildlife conservation. Assessing the sustainability of hunting has been a major goal in conservation biology but developing methods that accurately predict patterns of prey depletion has proven notoriously problematic. In this study, we sought to assess the sustainability of the hunting of indigenous Waiwai in Guyana by comparing results from the most commonly used static sustainability index, the production model, with results from spatially explicit biodemographic models for three indicator species; tapirs Tapirus terrestris, spider monkeys …

Crystal Structure Of Apobec3a Bound To Single-Stranded Dna Reveals Structural Basis For Cytidine Deamination And Specificity, Takahide Kouno, Tania V. Silvas, Brendan J. Hilbert, Shivender Shandilya, Markus-Frederik Bohn, Brian A. Kelch, William E. Royer, Mohan Somasundaran, Nese Kurt Yilmaz, Hiroshi Matsuo, Celia A. Schiffer

Celia A. Schiffer

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 A. This structure not only visualizes the active site …

Costs Of Group Locomotion: How Infant-Carrying And Group Members Mediate Walking Speed Decisions In North American And East African Populations, Leah M. Bouterse

Honors Projects

A major portion of humans’ activity-based energy expenditure is taken up by locomotion, particularly walking. Humans can offset the energetic expenditure of walking in numerous ways, both evolutionary (such as changes in body shape) and culturally. Behaviorally, people can choose to walk in a variety of ways, including alone or with a group, carrying loads, and walking quickly or more slowly. All of these behaviors have energetic outcomes and as such can be important windows into how populations and groups adjust to different constraints. While sex differences in speed of paired walkers have been established by others, the dynamics of …

Dynamic Functional Connectivity Reveals Temporal Differences In Wake And Stage-2 Sleep, Mazen El-Baba

Electronic Thesis and Dissertation Repository

The transition from wakefulness to sleep is marked by changes in neurophysiology, suggesting that changes in consciousness might be accompanied by changes in functional network organization. Brain activity of 21 healthy participants was measured via simultaneous EEG-fMRI as participants transitioned from wakefulness into sleep. All fMRI volumes were ICA-decomposed, yielding 42 neurophysiological sources. Independent component time courses were used to estimate mean functional connectivity (FC) and dynamic FC using a sliding window technique. Windowed matrices were submitted to k-means clustering (k = 7, L2-norm). Mean FC in Wake and Stage-2 Sleep (S2S) were similar. Dynamic analysis revealed differences in temporal …

A Genetic Signature Of The Evolution Of Loss Of Flight In The Galapagos Cormorant, Patricia Parker, Alejandro Burga, Weiguang Wang, Eyal Ben-David, Paul Wolf, Andrew Ramey, Claudio Verdugo, Karen Lyons, Leonid Kruglyak

Biology Department Faculty Works

We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in Caenorhabditis elegans and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential …

A Genetic Signature Of The Evolution Of Loss Of Flight In The Galapagos Cormorant, Patricia Parker, Alejandro Burga, Weiguang Wang, Eyal Ben-David, Paul C. Wolf, Andrew M. Ramey, Claudio Verdugo, Karen Lyons, Leonid Kruglyak

Patricia Parker

A Novel Population Of Cardiovascular Progenitors Persist In Neonates As Mesendodermal Cells, Julia Kim

Loma Linda University Electronic Theses, Dissertations & Projects

The rise in mortality due to cardiovascular disease has increased the need to develop an efficient regenerative therapeutic for heart failure. Numerous cell-based therapies have been investigated for myocardial regeneration; however, an optimal progenitor has yet to be discovered. Identifying a resident cell population with enhanced ability to differentiate into multiple lineages would greatly contribute to the field of stem cell-based regenerative therapy. Evidence suggests that endogenous cardiovascular progenitor cells (CPCs) that have been isolated from the heart itself express ISL1, KDR, and MESP1, and are capable of differentiating into all major cardiac lineages. The earlier developmental stage at which …

Molecular Evolution And Phylogeography Of Mitochondrial Dna Cytochrome B Gene In Southern California Santa Ana Speckled Dace (Rhinichthys Osculus), Pia Marie Vanmeter

Electronic Theses, Projects, and Dissertations

In this study, I sequenced the mitochondrial cytochrome b gene to elucidate the extent and pattern of genetic variations among and within populations of Rhinichthys osculus (Santa Ana Speckled Dace) found in the different watersheds in Southern California, Central California Coast and Eastern California Desert. I described and analyzed the structural characteristics and pattern of base sequence substitutions in the cytochrome b gene to understand the molecular evolution of the gene. The Phylogenetic analyses showed that the Southern California Santa Ana Speckled dace is a distinct population from the Central California Coast dace population and Eastern California Desert dace population, …

Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot

Electronic Thesis and Dissertation Repository

Despite the use of the host for dispersal by most parasite species, the extremely loose relationship typical between highly mobile hosts and generalist ectoparasites may lead to very different gene flow patterns between the two, leading in turn to different spatial genetic structure, and potentially different demographic history. I examined how similar gene flow patterns are between Cimex adjunctus, a generalist ectoparasite of bats present throughout North America, and two of its key bat hosts. I first analyzed the continent-scale genetic structure and demographic history of C. adjunctus and compared it to that of two of its hosts, the …

Human Evolution And Divine Agency, Alexandra Rakestraw

Dialogue & Nexus

Modern Christians often find themselves at a crossroads when confronted with the two predominant understandings of human and universal origins. Plain sense readings of Genesis lead many to believe in a historical six-day creation that occurred in the past ten thousand years while proponents on the other side of the spectrum use current scientific understanding to support a creation that occurs through evolutionary means. How one views human origins has a profound impact on one’s concept of how God works in the cosmos. In this paper, I will lay out a background to better understand the characters of Adam and …

Macrophages Are Necessary For Epimorphic Regeneration In African Spiny Mice, Jennifer Simkin, Thomas R. Gawriluk, John C. Gensel, Ashley W. Seifert

Biology Faculty Publications

How the immune system affects tissue regeneration is not well understood. In this study, we used an emerging mammalian model of epimorphic regeneration, the African spiny mouse, to examine cell-based inflammation and tested the hypothesis that macrophages are necessary for regeneration. By directly comparing inflammatory cell activation in a 4 mm ear injury during regeneration (Acomys cahirinus) and scarring (Mus musculus), we found that both species exhibited an acute inflammatory response, with scarring characterized by stronger myeloperoxidase activity. In contrast, ROS production was stronger and more persistent during regeneration. By depleting macrophages during injury, we demonstrate …

Disease Introduction By Aboriginal Humans In North America And The Pleistocene Extinction, Zachary D. Nickell, Matthew D. Moran

Journal of Ecological Anthropology

While overhunting and climate change have been the major hypotheses to explain the late-Pleistocene New World megafaunal extinctions, the role of introduced disease has only received brief attention. Here, we review pre-Columbian diseases endemic to aboriginal Americans and evaluate their potential to cause large-scale mortality in Pleistocene mammals. Of the probable communicable diseases present in pre-Columbian times, we regard anthrax and tuberculosis as viable candidates. These two diseases demonstrate characteristics that could have made them deadly to immunologically naïve populations. Introduced disease, as a primary cause or interacting with overhunting and climate change, could have contributed to the decline and …

Comparative Biogeography Of North American Pika Parasites: Unraveling A History Driven By Climate Change, Heather M. Toman

All NMU Master's Theses

Parasites are an understudied group that can provide important information on ecosystem dynamics and climate change as well as host biogeographic history. I performed a comparative biogeographic study on two endoparasitic helminth lineages associated with pikas (Ochotona) -the tapeworm genus Schizorchis and the pinworm subgenus Labiostomum (Eugenuris). Colonization history across Beringia was assessed using analyses of historical range estimation and tests for simultaneous divergence. Analysis results allow me reject the hypothesis that these parasites colonized the Nearctic during a single glacial cycle, as evidenced by multiple Nearctic and Palearctic lineage pairs that did not diverge simultaneously. This …

Secrets Of Sines: The Story Of Platy-1 Propagation In The Saimiri Lineage, Sarah Brantley

Honors Theses

No abstract provided.

Human-Nonhuman Chimeras, Ontology, And Dignity: A Constructivist Approach To The Ethics Of Conducting Research On Cross-Species Hybrids, Jonathan M. Vajda

The Hilltop Review

Developments in biological technology in the last few decades highlight the surprising and ever-expanding practical benefits of stem cells. With this progress, the possibility of combining human and nonhuman organisms is a reality, with ethical boundaries that are not readily obvious. These inter-species hybrids are of a larger class of biological entities called “chimeras.” As the concept of a human-nonhuman creature is conjured in our minds, either incredulous wonder or grotesque horror is likely to follow. This paper seeks to mitigate those worries and demotivate reasonable concerns raised against chimera research, all the while pressing current ethical positions toward their …

The Use Of Lactobacillus Salivarius L28 As A Bioprotective Culture In Dry Fermented Sausages, Kathy Flynt Collins

Theses and Dissertations--Animal and Food Sciences

A challenge study to validate a 5 log₁₀ CFU/g reduction of non-O157 Shiga-toxin producing Escherichia coli (STEC) in dry fermented sausage (DFS) was performed. A 4.49 ± 0.474 log₁₀ CFU/g was achieved over two trials. The results indicated that the process was not effective in reducing the pathogen to the level required of most pathogens by the USDA.

Lactobacillus salivarius L28 (L28) was screened in vitro for the ability to inhibit STEC utilizing the paper disk diffusion method. This strain is a known bacteriocin producer. The results revealed that L28 would be a good candidate for use as …

Archelosaurian Color Vision, Parietal Eye Loss, And The Crocodylian Nocturnal Bottleneck, Christopher A. Emerling

Biology

Vertebrate color vision has evolved partly through the modification of five ancestral visual opsin proteins via gene duplication, loss, and shifts in spectral sensitivity. While many vertebrates, particularly mammals, birds, and fishes, have had their visual opsin repertoires studied in great detail, testudines (turtles) and crocodylians have largely been neglected. Here I examine the genomic basis for color vision in four species of turtles and four species of crocodylians, and demonstrate that while turtles appear to vary in their number of visual opsins, crocodylians experienced a reduction in their color discrimination capacity after their divergence from Aves. Based on the …

Density-Dependent Foraging In Caenorhabditis Elegans, Joshua Greene

Student Theses and Dissertations

Game theory has long predicted that the density of competitors and their behaviors should affect foraging, and moreover suggests that multiple strategies can evolve and co-exist within a single species. I show that both of these predictions are met by foraging Caenorhabditis elegans. In Chapter 2, I show that animals alter their foraging behavior in response to population density, that certain pheromones induce this behavioral change, and that different wild isolates vary in response to the potent ascaroside icas#9. I use QTL mapping to find a major locus responsible for this variation, and map it to an icas#9 receptor, srx-43. …

Menageries Multiple: An Introduction To Zoological Multiplicity In The Modern American Zoo, Emily D. Gratke

Scripps Senior Theses

American zoological parks have been sites of intense consumer and scholar interest since their origination in the 20th century. Today, zoos reside at a tenacious hub of ideologies, practices, and priorities contributed to by various stakeholder groups. I propose that the foundational cause of this tension is zoological multiplicity: the theory that through human practices and perceptions, animals can embody multiple identities. Via an exploration of zoological multiplicity in American zoos with specific focus on zoo management, zoogoer, and animal activist stakeholder groups, this project proposes the widespread acknowledgment and understanding of zoological multiplicity as a method to improve animal …

Consciousness, Evidence, And Moral Standing, Irina Mikhalevich

Animal Sentience

Woodruff (2017) claims to have identified the neural correlates of phenomenal consciousness (“p-consciousness”) in fishes, and argues that these neurological data, along with behavioral evidence, suggest that teleost fishes are in all probability sentient organisms. Woodruff’s case may be strengthened by challenging key assumptions behind a common criticism of accounts such as his: that fishes cannot be p-conscious because they lack the cortical structures necessary for p-consciousness. A more serious objection to Woodruff’s proposal would be that his evidence for p-consciousness establishes only that fishes are “access-conscious” (“a-conscious”), where a-conscious states are cognitive representations that are made available to cognitive …