• Phylogenomics: Molecular Evolution in the Genomics Era

      Seetharam, Arun Somwarpet (2012-10-19)
      Evolutionary studies in recent years have been transformed by the development of new, powerful techniques for investigating many mechanisms and events of molecular evolution. Large collections of many different complete genomes now available in the public domain offer great advantages to genomic scale evolutionary studies. Phylogenomics, a term often used to describe the use of genomic scale data to infer species phylogeny or to predict protein function through evolutionary history, is greatly benefitted by the revolutionary progress in DNA sequencing technology. In the present study we developed and utilized various phylogenomic methods on large genome-scale data. In the first study, we applied Singular Value Decomposition (SVD) analysis to reexamine current evolutionary relationships for 12 Drosophila species using the predicted proteins from whole genomes. An SVD analysis on unfiltered whole genomes (193,622 predicted proteins) produced the currently accepted Drosophila phylogeny at higher dimensions, except for the generally accepted, but difficult to discern, sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. In the second study, we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species. Using the fragments generated by simulated digestion from the predicted targets of 16 Type IIB restriction enzymes, we sampled a large and effectively arbitrary selection of loci from these genomes. The resulting fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure, and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for these Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can improve studies of comparative genomics and the building of accurate phylogenetic trees. The third study utilized the relatively new Daphnia genome in an attempt to identify 40 orthologous groups of C2H2 Zinc-finger proteins that were previously determined to be well conserved in bilaterians. We identified 58 C2H2 ZFP genes in Daphnia that belong to these 40 distinct families. The Daphnia genome appears to be relatively efficient with respect to these well-conserved C2H2 ZFP, since only 7 of the 40 gene families have more than one identified member. Worms have a comparable number of 6. In flies and humans, C2H2 ZFP gene expansions are more common, since these organisms display 15 and 24 multi-member families respectively. In contrast, only three of the well-conserved C2H2 ZFP families have expanded in Daphnia relative to Drosophila, and in two of these cases, just one additional gene was found. The KLF/SP family in Daphnia, however, is significantly larger than that of Drosophila, and many of the additional members found in Daphnia appear to correspond to KLF 1/2/4 homologs, which are absent in Drosophila, but present in vertebrates. The last study was conducted to investigate the conservation and distribution of 38 C2H2 ZNF gene families in Eukaryotes. We combined two popular approaches for homolog detection, Reciprocal Best Hit (RBH) and Hidden–Markov model (HMM) profile search, on a diverse set of complete genomes of 124 eukaryotic species ranging from excavates to humans. We succeeded in identifying 3,675 genes as distinct members of the 38 C2H2 gene families. This largely automated technique is much faster than manual methods and is able to detect homologs accurately and efficiently among a diverse set of organisms. Our analysis of the 38 evolutionarily conserved C2H2 ZNF gene families revealed a stepwise appearance of ZNF families, agreeing well with the phylogenetic relationship of the organisms compared and their presumed stepwise increase in complexity.
    • A self improvement sheet for biology teachers in the secondary schools

      Roberts, Ernestine Winifred (2013-01-22)
      Not available
    • Cloning and Characterization of Hypothetical Exported Proteins from Community Associated Staphylococcus Aureus

      Kaur, Haninder (2013-01-30)
      Methicillin resistant Staphylococcus aureus (MRSA), a major cause of nosocomial infections, has acquired resistance to beta-lactam and other antibiotics. Recently, community associated MRSA (CA-MRSA) has developed independent of hospital associated MRSA (HA-MRSA). One of the major differences between the hospital and community strains is that the former is multi-resistant to antibiotics while the latter is not as resistant but is significantly more invasive. This increased invasiveness and the ability to cause life-threatening infections, even in immunocompetent individuals, makes CA-MRSA critically important as a public health problem. CA-MRSA is known to cause skin and soft tissue infections; bacteria interact with host skin cells and gain access to deeper tissues causing invasive infections. During this process the bacteria may secrete proteins that aid in the interaction with the host by adhering, invading or causing host cell death and lysis. To understand the virulence mechanisms involved in invasion, we investigated genes described as hypothetical proteins in MSSA476. The bioinformatics-selected proteins showed high probability of being secreted and most were unique to CA-MRSA. Our analysis showed 24 such genes. This study shows primer design for 15 of the genes (7 of the 24 had already been cloned in our laboratory). Using gateway cloning, the 15 genes were cloned into BL-21 expression clones. CA-MRSA’s are known for causing invasive skin infections. To further understand the involvement of our proteins of interest in invasion, human keratinocyte cell lines were used in a study of virulence and interaction with skin. To understand the involvement of our hypothetical secreted proteins, we investigated the mRNA expression level, using RT-qPCR and Livak method, of 20 hypothetical exported proteins in presence of human dermal keratinocyte cell line. Our investigation revealed two genes that showed increased mRNA expression in the presence of keratinocytes, which may be due to factors associated with keratinocytes that may have triggered increased mRNA expression. Keratinocytes are capable of forming cell-cell junctions and producing antimicrobial peptides and cytokines in response to microbes. The increased mRNA expression of two genes may be towards binding to junctions for invasion or may be expressed in response to antimicrobial peptides or cytokines.
    • Characterization of Novel Extracellular Matrix (Ecm) Proteins (Mgp and Lumican) and Their Implications in Vascular Development, Angiogenesis, and Cancer

      Sharma, Bikram (2013-01-30)
      Extracellular matrix (ECM) constitutes a large component of our tissue structure. Primarily, ECM provides structural and adhesive support to our cells, but it also controls cellular signaling and behavior. Homeostasis of extracellular matrix composition and function is maintained by our body through a balanced synthesis, degradation and remodeling of ECM. However, under pathological conditions and genetic mutations, ECM homeostasis is disrupted due to deregulation in ECM synthesis, assembly, remodeling, and degradation. A number of diseases, including cardiovascular diseases and cancer, are found to occur due to alterations in ECM. Therefore, targeting ECM can be an attractive therapeutic approach to treat these diseases, and it requires our complete understanding of the ECM molecules and the molecular mechanism it employs in controlling cellular functions. To this end, this study is aimed at the characterization of two ECM proteins—Matrix Gla Protein (MGP) and Lumican—for their roles in vascular development, angiogenesis, and cancer. Findings from this study show that MGP is a critical ECM regulator that promotes angiogenic resolution by suppressing endothelial sprouting and stabilizing vascular lumen formation. In addition, MGP also inhibits tumor growth by inhibiting tumor angiogenesis. On the other hand, our findings show Lumican suppresses tumor growth and has anti-angiogenic activity in a context specific manner.
    • A morphological and cultural study of a species of Nigrospora

      Patrick, Mildred (2013-03-08)
      Not Available.
    • Levels of Selection in a Polymorphic Species

      Korody, Marisa L. (2013-09-05)
      Phenotype is affected by many factors, including but not limited to environment, conspecifics, and genetics. Evidence of phenotypic variation is everywhere, some of which is controlled solely by environment, and others that are fixed by genetics. Genetic polymorphisms are rare, but very useful for the study of selection and genetics. These genetic polymorphisms provide a phenotypic link to the underlying genetics and are even more useful when there are associated behavioral differences. I examine multiple levels of selection that are acting upon a polymorphic passerine, the white-throated sparrow (Zonotrichia albicollis). Males and females of this species occur in two morphs, white or tan, based upon the color of their crown strips. This plumage polymorphism is absolutely correlated with a complex chromosomal rearrangement on the second largest autosome. Within this dissertation I explore how climate needs to be addressed in ecological studies to fully understand the mechanisms behind variation. I explore whether sexual selection is acting within this species and the differences between the morphs through the use of Bateman Gradients. Darwin suggested that sex ratios influence sexual selection, but what about morph ratios? I examine the frequency variation of morphs within this species. Variation in morph production may be favored by a potential tradeoff between the number of males and the number of white offspring produced in a clutch that suggests greater costs associated with producing white morph individuals. Mendelian segregation is inconsistent in this species, and transmission distortion may contribute to morph ratio variation. I show that white male sperm varies in production from 0% - 100% white sperm/individual consistent with transmission distortion. Finally, candidate gene mapping was used to identify the genes sequestered in this rearrangement that may be responsible for the polymorphism and the evolution behind the rearrangement.
    • Summer Indiana Bat Ecology in the Southern Appalachians: An Investigation of Thermoregulation Strategies and Landscape Scale Roost Selection

      Hammond, Kristina (2014-03-18)
      In the southern Appalachians there are few data on the roost ecology of the federally endangered Indiana bat (Myotis sodalis). During 2008-2012, we investigated roosting ecology of the Indiana bat in ~280,000 ha in the Great Smoky Mountains National Park, Cherokee National Forest, and Nantahala National Forest in the southern Appalachians Mountains of Tennessee and North Carolina. We investigated 2 aspects of the Indiana bat’s roosting ecology: thermoregulation and the extrinsic factors that influence body temperature, and landscape-scale roost selection. To investigate thermoregulation of bats at roost, we used data gathered in 2012 from 6 female Indiana bats (5 adults and 1 juvenile) to examine how reproductive condition, group size, roost characteristics, air temperature, and barometric pressure related to body temperature of roosting bats. We found that air temperature was the primary factor correlated with bats’ body temperatures while at roost (P < 0.01), with few differences detected among reproductive classes in terms of thermoregulatory strategies. To understand how Indiana bats select roosts on a landscape-scale, we created a presence-only model through the program MaxENT using 76 known roost locations to identify areas important to summer roosting habitat within our study area and to identify important landscape-scale factors in habitat selection. The final model showed that Indiana bats selected roosts on the upper portion of ridges on south facing slopes in mixed pine-hardwood forests at elevations of 260-700 meters. Unfortunately, due to small sample size and the large effort required to fully investigate thermoregulation of Indiana bats in the southern Appalachians, we only were able run correlations with temperature data, and further investigation is needed to make concrete conclusions. However, the new advancements in resolution of landscape cover data and new programs in spatial modeling have enabled us to produce a large scale spatial model for identifying Indiana bat summer roosting habitat within our study area. Our findings have added to our understanding of Indiana bat roosting ecology, particularly in the southern Appalachian Mountains, and will aid land managers in effective management for this federally endangered species.
    • Evaluation of an Avian Radar System

      Gerringer, Michael B. (2014-03-18)
      The problem of bird strikes in aviation is becoming an increasing threat, both to aircraft and to human safety. Management efforts have reduced wildlife hazards below 500 feet and within the immediate airport environment, but traditional methods of monitoring bird activity are limited to an observer’s field of view. Avian radar systems could potentially be useful in monitoring bird activity at great distances from the airport, at higher altitudes, and at night (Dolbeer 2006), but little work has been done to validate the tracking capabilities of avian radar systems. Thus, the goal of this research is to evaluate the detection and tracking abilities of the Merlin Avian Radar System provided by DeTect Inc. Radio-controlled (RC) aircraft flights were used to systematically test the tracking abilities of the Merlin System with respect to distance and altitude. Transits by free-flying birds provided an equally important test of the Merlin System, allowing for the assessment of tracking performance as influenced by flock size, altitude, and distance from the radar unit. Overall tracking performance regarding the RC aircraft and single large bird targets was poor across all study distances and altitudes. However, flocks of large birds such as geese and cranes were tracked well, even those several miles away from the radar unit. Given these results, avian radar could be a useful tool for monitoring bird flock activity at airports, but less so for single large bird targets such as thermalling raptors.
    • Diurnal and nocturnal avian antipredator behavior in thermally challenging conditions

      Carr, Jennie M. (2014-03-18)
      Diurnal avian antipredator behavior has been the focus of much past research, yet the influence of the thermal environment on such behaviors is often overlooked. Far less is known about nocturnal avian antipredator behavior, including how these behaviors are influenced by challenging thermal environments. The first portion of my research focused on how the thermal environment influences the diurnal antipredator behavior of wintering birds while (i) exposed to high wind speeds, (ii) foraging in sunlit and shaded microhabitats, and (iii) when using thermoregulatory postures to conserve body heat. In addition to increasing convective heat loss, high wind speeds increase the prevalence of background movements in the environment. My research demonstrated that wintering sparrows exposed to a moving stimulus are less likely to flush to cover on windy days than on calm days, suggesting that wind-driven visual noise may interfere with predator detection. Predator detection may also vary when feeding in sunlight and shade, and the thermal benefits of foraging in direct sunlight on cold winter days may also play an important role in dictating microhabitat choice. Regardless of the thermal benefits of foraging in sunlight, wintering sparrows preferred to feed in shaded microhabitats even at ambient temperatures well below thermoneutrality. However, these birds foraged in sunlight more frequently as ambient temperatures fell, suggesting a trade-off between thermoregulation (solar input) and predation risk. Additional evidence of such a thermoregulation-predation trade-off was evident in the use of heat-conserving thermoregulatory postures by wintering sparrows. Fluffing the feathers or standing on one foot will reduce the amount of heat lost to the environment. However, such postures slow take-off time and likely result in an increase in predation risk. As such, these risky postures were only used when feeding at relatively low ambient temperatures and when near protective cover. In general, these results indicate that characteristics of the thermal environment play an important role in dictating diurnal antipredator behavior. To address how the thermal environment influences nocturnal avian antipredator behavior, I examined the predation-related costs of using energy-saving nocturnal hypothermia. Many species of birds reduce their nighttime body temperature, thus reducing metabolic rate and conserving energy. Such drops in body temperature may be quite substantial and likely influence a bird’s ability to respond to a potential threat during the night. To examine the potential costs of hypothermia, I conducted nocturnal flight tests on hypothermic mourning doves (Zenaida macroura). In general, doves that cooled by more than 5 °C flew poorly or were unable to fly, but were able to fly well once re-warmed to near their normal daytime body temperatures. Thus, low body temperatures during energy-saving hypothermia likely result in an increase in the risk of nocturnal predation. Nocturnal antipredator behavior was also examined in ruby-throated hummingbirds (Archilochus colubris). These hummingbirds frequently use nocturnal torpor (i.e., deep hypothermia), with significant reductions in body temperature and corresponding inability to respond behaviorally to external stimuli. Although hummingbirds altered torpor use seasonally and over the course of the observation period, hummingbirds did not consistently reduce their use of torpor following an experimental increase in perceived predation risk. Thus, although hypothermia is behaviorally costly, further studies are needed to clarify the role of predation on nocturnal behavior in birds.
    • Using Stable Isotope Analysis to Study Altitudinal and Latitudinal Bat Migration

      Arias, Lily (2014-10-03)
      The general lack of knowledge on basic aspects of the biology of temperate and tropical bats, their low reproductive rates, and threats such as white nose syndrome, wind farms, and habitat loss, make them very susceptible to population declines.My research uses an innovative technique, the analysis of stable isotopes, to study the ecology of bat migration with the main goals of contributing significantly to the understanding of bat biology and assessing the conservation status and susceptibility of bats. In the first chapter,I measured the content of hydrogen isotopes in fur samples of migratory bat species killed at a wind farm in northern Indiana to determine their geographic origin.North American tree bats ( Lasiurus borealis, L. cinereus,and Lasionycteris noctivagans)are considered long distance migrants. In North America, peaks in bat mortality at wind farms occur between mid-July and mid-September. This period is associated with fall migration of bats from their summer (breeding) grounds to their wintering grounds. Thus, wind turbines may have serious negative effects on a strategic event in the life of bats by interrupting migratory connectivity and thereby imperiling the long-term persistence of migratory bat species at large scales.The analysis accurately predicted the known origin of control samples and estimated that non-control bats killed at the wind farm originated from several populations in the United States as well as in Canada. My results highlighted the threat of wind farms to local bat populations as well as to bats originating far from those farms, and emphasized the need for conservation policies across borders.High variation in stable hydrogen isotopes in migrant individuals of all 3 species was observed, suggesting that individuals or populations from a variety of regions pass through the wind farm. In the second chapter,I evaluated the triple-isotopic (hydrogen, carbon, and nitrogen) composition of the tissues of 7 bat species collected at 3 altitudes in the Central Andes of Peru,and the variation of these isotopes across an altitudinal gradient,the application of isotope analysis to migration studies, and trophic effect. Previous studies had demonstrated that iv hydrogen isotopes were a reliable tool to track altitudinal movements of birds, and there was evidence from soil and plant studies that nitrogen and carbon isotopes could serve the same purpose. However, studies focused on bats were lacking. Hydrogen and nitrogen isotopes in the sanguinivorous control were found to be enriched relative to those of the syntopic frugivores.Carbon isotopes in the sanguinivorous bat were depleted when compared to frugivores.Differences in hydrogen found between trophic groups are the first reported for the species studied and support results found elsewhere in the Neotropics.My results demonstrated that, in spite of the wide array of physiological and environmental factors producing temporal and spatial variation, the analysis of hydrogen isotopes is a promising tool to study altitudinal movements of bats when used over long distances. Neither stable isotopes of nitrogen or carbon appear to be reliable to track movements along short gradients such as those along mountains. The contrast of these findings with the results of previous studies suggests that isotopic gradients may be specific to given taxon and localities.My results contributed to the understanding of bat movement patterns and therefore to assessing their sensitivity to potential threats such as habitat loss and connectivity.
    • Acoustic Communication in the Temperate Treefrogs Pseudacris Crucifer and Acris Crepitans

      Keating, John (2015-01-07)
      Spring peepers and cricket frogs produce advertisement calls to attract females. As ectotherms their body temperatures are greatly affected by ambient air temperature. Some characteristics of their advertisement calls are correlated with temperature. I analyzed advertisement calls of both species recorded in western-central Indiana. I compared call characteristic correlations with temperature found in our populations to those in populations in other geographic areas and found similar trends throughout the range of both species. Secondly, I examined aggressive calls in the spring peepers. Aggressive calls are used in male-male interactions, and in the spring peeper are a distinct call type different from advertisement calls in two characteristics. I used a habituation-discrimination protocol to test which of the two call characteristics, that differ between advertisement and aggressive calls, males use to distinguish advertisement and aggressive calls. I found that males responded with intermediate aggression to calls that only differ from advertisement in one of the two characteristics and responded with the most aggression to calls that differed from advertisement calls in both characteristics.