Life Sciences Commons^™

A Tale Of Two Genomes: The Complex Interplay Between The Mitochondrial And The Nuclear Genomes, Abhilesh S. Dhawanjewar

School of Biological Sciences: Dissertations, Theses, and Student Research

Mitochondria, the product of an ancient endosymbiotic event are pivotal to eukaryotic cells by synthesizing the majority of the cell’s ATP output. However, modern- day mitochondria are completely dependent on more than one thousand nuclear-encoded products for their function and the maintenance of their genomes. The fundamentally different ways in which the mitochondrial (mtDNA) and the nuclear (nucDNA) genomes are replicated and inherited lead to captivating coevolutionary dynamics between them. The aims of this dissertation are to investigate the coevolutionary dynamics between the mitochondrial and nuclear genomes at three distinct biological scales. At the organismal level, we use a Drosophila …

Stepping-Stones And Mediators Of Pandemic Expansion: A Context For Humans As Ecological Super-Spreaders, Eric P. Hoberg, Walter A. Boeger, Daniel R. Brooks, Valeria Trivellone, Salvatore J. Agosta

MANTER: Journal of Parasite Biodiversity

Humans represent ecological super-spreaders in the dissemination and introduction of pathogens. These processes, consistent with the dynamics of the Stockholm paradigm, are exemplified in the origin and globalized distributions of SARS-CoV-2 since initial recognition in central Asia during 2019 and 2020. SARS-like viruses are not widespread in mammals but appear widespread in chiropterans. Bats are isolated ecologically from most other assemblages of mammals in terrestrial systems. Humans may be the stepping-stone hosts for broad global dissemination and wider infection (given the opportunity) among diverse assemblages of mammals in which host and viral capacity are compatible. Human globalization mediated insertion in …

Frugivory And Seed Dispersal By Carnivorans, John P. Draper, Julie K. Young, Eugene W. Schupp, Noelle G. Beckman, Trisha B. Atwood

USDA Wildlife Services: Staff Publications

Seed dispersal is critical to the ecological performance of sexually reproducing plant species and the communities that they form. The Mammalian order Carnivora provide valuable and effective seed dispersal services but tend to be overlooked in much of the seed dispersal literature. Here we review the literature on the role of Carnivorans in seed dispersal, with a literature search in the Scopus reference database. Overall, we found that Carnivorans are prolific seed dispersers. Carnivorans’ diverse and plastic diets allow them to consume large volumes of over a hundred families of fruit and disperse large quantities of seeds across landscapes. Gut …

Late Pleistocene Megafauna Extinction Leads To Missing Pieces Of Ecological Space In A North American Mammal Community, Felisa A. Smith, Emma A. Elliott Smith, Amelia Villaseñor, Catalina P. Tomé, S. Kathleen Lyons, Seth D. Newsome

School of Biological Sciences: Faculty Publications

The conservation status of large-bodied mammals is dire. Their decline has serious consequences because they have unique ecological roles not replicated by smaller-bodied animals. Here, we use the fossil record of the megafauna extinction at the terminal Pleistocene to explore the consequences of past biodiversity loss. We characterize the isotopic and body-size niche of a mammal community in Texas before and after the event to assess the influence on the ecology and ecological interactions of surviving species (>1 kg). Preextinction, a variety of C₄ grazers, C₃ browsers, and mixed feeders existed, similar to modern African savannas, with …

Genomic Approaches To Uncovering The Coevolutionary History Of Parasitic Lice [Review], Kevin P. Johnson

Harold W. Manter Laboratory: Library Materials

Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among …

Molecular Adaptation To Folivory And The Conservation Implications For Madagascar’S Lemurs, Elaine E. Guevara, Lydia K. Greene, Marina B. Blanco, Casey Farmer, Jeannin Ranaivonasy, Joelisoa Ratsirarson, Karine L. Mahefarisoa, Tsiky Rajaonarivelo, Hajanirina H. Rakotondrainibe, Randall E. Junge, Cathy V. Williams, Elodi Rambeloson, Hoby A. Rasoanaivo, Vololonirina Rahalinarivo, Laza H. Andrianandrianina, Jonathan B. Clayton, Ryan S. Rothman, Richard R. Lawler, Brenda J. Bradley, Anne D. Yoder

Department of Food Science and Technology: Faculty Publications

The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases …

Overview Of The Insect Food And Feed Industry, Daniel J. Seckman

Department of Entomology: Distance Master of Science Projects

The entomophagy field is one that when you immerse yourself in it, you will feel like the entire world is talking about insects as food and feed. Yet, from the outside, the industry is virtually nonexistent. In the United States, the North American Coalition for Insect Agriculture (NACIA) is the leading organization dedicated to growing the insect food and feed sector. While the organization has grown extensively in recent years, most individuals in the food, feed, and entomological industry have never heard of the organization. The Wall Street Journal presents the annual Food Forum, which aims to “tackle the critical …

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 …

Methylation-Based Enrichment Facilitates Low-Cost, Noninvasive Genomic Scale Sequencing Of Populations From Feces, Kenneth L. Chiou, Christina M. Bergey

Public Health Resources

Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particularly at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by bacterial and other non-host DNA. The high proportion of non-host DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. To address this issue, we developed an inexpensive capture method for enriching host DNA from noninvasive fecal samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate …

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 …

Nematodes Associated With Mammals In The Great American Biotic Interchange (Gabi), F. Agustin Jimenez, Juliana Notarnicola, Scott Lyell Gardner

Scott L. Gardner Publications

The Great American Biotic Interchange (GABI) is a large-scale zoogeographic event that illustrates the exchange and diversification of mammals between North and South America. This phenomenon was accelerated by the connection of both landmasses during the Pliocene. Support for this phenomenon includes the extant distribution of xenarthrans, didelphiomorph marsupials, hystricognath and cricetine rodents, sciurids and carnivores, as well as the distribution of fossils in the stratigraphic record and the coalescence of genotypes. Contrasting with the relatively well-documented role and history of mammals in GABI, the role of their parasites has been largely neglected. As a consequence, the reconstructions of the …

Assessing The Archaeoparasitological Potential Of Quids As A Source Material For Immunodiagnostic Analyses, Johnica J. Morrow, Karl Reinhard

Karl Reinhard Publications

In the present study, quids from La Cueva de los Muertos Chiquitos (CMC) were subjected to ELISA tests for 2 protozoan parasites, Toxoplasma gondii (n=45) and Trypanosoma cruzi (n=43). The people who occupied CMC, the Loma San Gabriel, lived throughout much of present-day Durango and Zacatecas in Mexico. The known pathoecology of these people puts them into at-risk categories for the transmission of T. gondii and T. cruzi. Human antibodies created in response to these 2 parasites can be detected in modern saliva using ELISA kits intended for use with human serum. For these reasons, quids were reconstituted and …

Temporal And Spatial Distribution Of Enterobius Vermicularis (Nematoda: Oxyuridae) In The Prehistoric Americas, Karl J. Reinhard, Adauto Araújo, Johnica J. Morrow

Karl Reinhard Publications

Investigations of Enterobius sp. infection in prehistory have produced a body of data that can be used to evaluate the geographic distribution of infection through time in the Americas. Regional variations in prevalence are evident. In North America, 119 pinworm positive samples were found in 1,112 samples from 28 sites with a prevalence of 10.7%. Almost all of the positive samples came from agricultural sites. From Brazil, 0 pinworm positive samples were found in 325 samples from 7 sites. For the Andes region, 22 pinworm positive samples were found in 411 samples from 26 sites for a prevalence of 5.3%. …

Paleoepidemiology Of Intestinal Parasites And Lice In Pre-Columbian South America *, Adauto Araujo, Karl J. Reinhard, Daniela Leles, Luciana Sianto, Alena Iniguez, Martin Fugassa, Berrnardo Arriaza, Nancy Orellana, Luiz Fernando Ferreira

Karl Reinhard Publications

Some human parasites originated in prehominid ancestors in Africa. Nematode species, such as Enterobius vermicularis (pinworm), hookworms and Trichuris trichiura are shared by humans and other close phylogenetic primates (Pan and Gorilla), showing that they infected a common ancestor to this group. When humans migrated from Africa to other continents they carried these parasites wherever climate conditions allowed parasite transmission from host to host. Other parasites, however, were acquired throughout human biological and social evolutive history when new territories were occupied. Paleoparasitology data is a valuable source to recover emergence and disappearance of parasite infections through analysis of archaeological remains. …

Gene Turnover In The Avian Globin Gene Families And Evolutionary Changes In Hemoglobin Isoform Expression, Juan C. Opazo, Federico G. Hoffmann, Chandrasekhar Natarajan, Christopher C. Witt, Michael Berenbrink, Jay F. Storz

School of Biological Sciences: Faculty Publications

The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α₂β₂ protein responsible for blood-O₂ transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during …

Network Analysis Of Host–Virus Communities In Bats And Rodents Reveals Determinants Of Cross-Species Transmission, Angela D. Luis, Thomas J. O'Shea, David T.S. Hayman, James L.N. Wood, Andrew A. Cunningham, Amy T. Gilbert, James N. Mills, Colleen T. Webb

USDA Wildlife Services: Staff Publications

Bats are natural reservoirs of several important emerging viruses. Cross-species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross-species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We …

Paleoparasitology – Human Parasites In Ancient Material, Adauto Araújo, Karl Reinhard, Luiz Fernando Ferreira

Karl Reinhard Publications

Parasite finds in ancient material launched a new field of science: paleoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and paleontological remains, some preserved for millions of years by fossilization. However, the paleoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a …

Discovery Of A 240 Million Year Old Nematode Parasite Egg In A Cynodont Coprolite Sheds Light On The Early Origin Of Pinworms In Vertebrates, Jean-Pierre Hugot, Scott Gardner, Victor Borba, Priscilla Araujo, Daniela Leles, Átila Da-Rosa, Juliana Dutra, Luis Fernando Ferreira, Adauto Araújo

Harold W. Manter Laboratory of Parasitology: Faculty and Staff Publications

Background: We report the discovery of a nematode parasite egg (Nemata: Oxyurida) from a coprolite closely associated with the remains of several species of Cynodontia, dated to 240 million years old. This finding is particularly significant because this is the oldest record of an oxyurid nematode yet discovered, and because the cynodonts are considered a stem-group of the mammals.

Methods: We extracted material from a fully mineralized coprolite by both scraping the surface, and removing fragments from its interior with clean dental instruments used a single time. A single drop of glycerol from a new vial was added as a …

The Origin And Molecular Evolution Of Two Multigene Families: G-Protein Coupled Receptors And Glycoside Hydrolase Families, Seong-Il Eyun

School of Biological Sciences: Dissertations, Theses, and Student Research

Multigene family is a group of genes that arose from a common ancestor by gene duplication. Gene duplications are a major driving force of new function acquisition. Multigene family thus has a fundamental role in adaptation. To elucidate their molecular evolutionary mechanisms, I chose two multigene families: chemosensory receptors and glycoside hydrolases. I have identified complete repertoires of trace amine-associated receptors (TAARs), a member of chemosensory receptors, from 38 metazoan genomes. An ancestral-type TAAR emerged before the divergence between gnathostomes (jawed vertebrates) and sea lamprey (jawless fish). Primary amine detecting TAARs (TAAR1-4) are found to be older and have evolved …

The Role Of Gnrh-Ii And Its Receptor In Testicular Function, Amy Desaulniers

Department of Animal Science: Dissertations, Theses, and Student Research

The second mammalian isoform of GnRH (GnRH-II) has been linked to regulation of cell proliferation, feed intake, and the interaction between energy balance and reproductive behavior. In contrast to the native form of GnRH (GnRH-I), GnRH-II is an inefficient modulator of gonadotropin secretion. Unlike many species, a functional receptor (GnRHR-II) specific to this ligand has been discovered in the pig that may be directly involved in testosterone production. Therefore, our objective was to identify the role of GnRH-II and its receptor in testicular function. First, there was 6-fold more GnRHR-II protein in the testis than anterior pituitary gland of boars. …

An Incompatibility Between A Mitochondrial Trna And Its Nuclear-Encoded Trna Synthetase Compromises Development And Fitness In Drosophila, Colin D. Meiklejohn, Marissa A. Holmbeck, Mohammed A. Siddiq, Dawn N. Abt, David M. Rand, Kristi L. Montooth

School of Biological Sciences: Faculty Publications

Mitochondrial transcription, translation, and respiration require interactions between genes encoded in two distinct genomes, generating the potential for mutations in nuclear and mitochondrial genomes to interact epistatically and cause incompatibilities that decrease fitness. Mitochondrial-nuclear epistasis for fitness has been documented within and between populations and species of diverse taxa, but rarely has the genetic or mechanistic basis of these mitochondrial–nuclear interactions been elucidated, limiting our understanding of which genes harbor variants causing mitochondrial–nuclear disruption and of the pathways and processes that are impacted by mitochondrial–nuclear coevolution. Here we identify an amino acid polymorphism in the Drosophila melanogaster nuclear-encoded mitochondrial tyrosyl–tRNA …

‘‘Megavirales’’, A Proposed New Order For Eukaryotic Nucleocytoplasmic Large Dna Viruses, Philippe Colson, Xavier De Lamballerie, Natalya Yutin, Sassan Asgari, Yves Bigot, Dennis K. Bideshi, Xiao-Wen Cheng, Brian A. Federici, James L. Van Etten, Eugene V. Koonin, Bernard La Scola, Didier Raoult

Nebraska Center for Virology: Faculty Publications

The nucleocytoplasmic large DNA viruses (NCLDVs) comprise a monophyletic group of viruses that infect animals and diverse unicellular eukaryotes. The NCLDV group includes the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Mimiviridae and the proposed family ‘‘Marseilleviridae’’. The family Mimiviridae includes the largest known viruses, with genomes in excess of one megabase, whereas the genome size in the other NCLDV families varies from 100 to 400 kilobase pairs. Most of the NCLDVs replicate in the cytoplasm of infected cells, within so-called virus factories. The NCLDVs share a common ancient origin, as demonstrated by evolutionary reconstructions that trace approximately 50 genes encoding …

A Comparison Of Bats And Rodents As Reservoirs Of Zoonotic Viruses: Are Bats Special?, Angela D. Luis, David T. S. Hayman, Thomas J. O'Shea, Paul M. Cryan, Amy T. Gilbert, Juliet R. C. Pulliam, James N. Mills, Mary E. Timonin, Craig K. R. Willis, Andrew A. Cunningham, Anthony R. Fooks, Charles E. Rupprecht, James L. N. Wood, Colleen T. Webb

USDA Wildlife Services: Staff Publications

Bats are the natural reservoirs of a number of high-impact viral zoonoses. We present a quantitative analysis to address the hypothesis that bats are unique in their propensity to host zoonotic viruses based on a comparisonwith rodents, another important host order. We found that bats indeed host more zoonotic viruses per species than rodents, and we identified life-history and ecological factors that promote zoonotic viral richness. More zoonotic viruses are hosted by species whose distributions overlap with a greater number of other species in the same taxonomic order (sympatry). Specifically in bats, therewas evidence for increased zoonotic viral richness in …

Worms, Nematoda, Scott Lyell Gardner

Scott L. Gardner Publications

Nematodes are the most speciose phylum of metazoa on earth. Not only do they occur in huge numbers as parasites of all known animal groups, but also they are found in the soils, as parasites of plants, and in large numbers in the most extreme environments, from the Antarctic dry valleys to the benthos of the ocean. They are extremely variable in their morphological characteristics, with each group showing morphological adapta­tions to the environment that they inhabit. Soil-dwelling forms are extremely small; many marine species have long and complex setae; and parasitic species man­ifest amazingly great reproductive potential and large …

Review: Mammals Of Colorado. Second Edition. David M. Armstrong, James P. Fitzgerald, And Carron A. Meaney., Thomas J. O'Shea

The Prairie Naturalist

In my view, the second edition of Mammals of Colorado is among the finest state-level books on mammals available. The book is a major revision of the first edition (Fitzgerald et al. 1994) and is a reference worth having, even if the first edition is already at hand. In this review, T summarize aspects of the new volume and provide comparisons to the first edition in an effort to persuade the reader that this is indeed the case.

The first four chapters of the second edition include background information and updated material about Colorado environments, mammals in general, the history …

Composition And Evolution Of The Vertebrate And Mammalian Selenoproteomes, Marco Mariotti, Perry G. Ridge, Yan Zhang, Alexei V. Lobanov, Thomas H. Pringle, Roderic Guigo, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Background: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24.

Methodology/Principal Findings: We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian …

First Stable Isotope Analysis Of Asiatic Wild Ass Tail Hair From The Mongolian Gobi, Micha Horacek, Petra Kaczensky, Merina Burnik Sturm

Erforschung biologischer Ressourcen der Mongolei / Exploration into the Biological Resources of Mongolia, ISSN 0440-1298

Stable isotope analysis has become a powerful tool to study feeding ecology, water use or movement pattern in contemporary, historic and ancient species. Certain hair and teeth grow continuously, and when sampled longitudinally can provide temporally explicit information on dietary regime and movement pattern. In an initial trial, we analysed a tail sample of an Asiatic wild ass (Equus hemionus) from the Mongolian Gobi. We found seasonal variations in H, C, and N isotope patterns, likely being the result of temporal variations in available feeds, water supply and possibly physiological status. Thus stable isotope analysis shows promise to …

Synthesizing Parasitology With Archaeology In Paleopathology, Karl Reinhard, Adauto Araujo

Karl Reinhard Publications

Parasitology is the study of organisms that are symbiotic with other organisms. In this form of symbiosis, the parasite species by definition benefits from the interaction while the host is harmed to some degree. In actuality, some parasites benefit their hosts. The animals traditionally studied by parasitologists range from protozoa to arthropods, and include all types of internal and external worms. Ticks, fleas, lice, and a variety of insects that transmit parasites are also studied by parasitologists. Recently, a more holistic view of parasitism appeared, including bacteria and viruses. In essence, parasitology is the study of a certain kind of …

Phylogenetic Diversification Of The Globin Gene Superfamily In Chordates, Jay F. Storz, Juan C. Opazo, Federico G. Hoffmann

Jay F. Storz Publications

Phylogenetic reconstructions provide a means of inferring the branching relationships among members of multigene families that have diversified via successive rounds of gene duplication and divergence. Such reconstructions can illuminate the pathways by which particular expression patterns and protein functions evolved. For example, phylogenetic analyses can reveal cases in which similar expression patterns or functional properties evolved independently in different lineages, either through convergence, parallelism, or evolutionary reversals. The purpose of this article is to provide a robust phylogenetic framework for interpreting experimental data and for generating hypotheses about the functional evolution of globin proteins in chordate animals. To do …

Giant Viruses, James L. Van Etten

James Van Etten Publications

The common view of viruses, mostly true, is of tiny burglars that sneak into cells, grab the biosynthetic controls and compel the cell to make huge numbers of progeny that break out of the cell and keep the replication cycle going. Viruses are supposed to be diminutive even compared to cells that are just a micrometer (1,000 nanometers) in diameter. They are supposed to travel light, making do with just a few well-adapted genes.

In 1992, a new microorganism was isolated from a power-plant cooling tower in Bradford, England, where Timothy Robotham, a microbiologist at Leeds Public Health Laboratory, was …