Life Sciences Commons^™

Protocol For An Agent-Based Model Of Recombination In Bacteria Playing A Public Goods Game, Isaiah Paolo A. Lee, Omar T. Eldakar, J. Peter Gogarten, Cheryl P. Andam

Biology Faculty Articles

Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory.

For complete details on the use and execution of this protocol, please refer to Lee et al.¹

Microbiome Analyses Demonstrate Specific Communities Within Five Shark Species, Rachael Storo, Cole Easson, Mahmood S. Shivji, Jose V. Lopez

Biology Faculty Articles

Profiles of symbiotic microbial communities (“microbiomes”) can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in South Florida (nurse, lemon, sandbar, Caribbean reef, and tiger) have been characterized for the first time. The microbiomes show species specific microbiome composition, distinct from surrounding seawater. Shark anatomical location (gills, teeth, skin, cloaca) affected the diversity of microbiomes. An in-depth analysis of teeth communities revealed species specific microbial communities. For example, the genus Haemophilus, explained 7.0% of the differences of the teeth microbiomes …

Social Familiarity Improves Fast-Start Escape Performance In Schooling Fish, Lauren E. Nadler, Mark I. Mccormick, Jacob L. Johansen, Paolo Domenici

Marine & Environmental Sciences Faculty Datasets

Using social groups (i.e. schools) of the tropical damselfish Chromis viridis, we tested how familiarity through repeated social interactions influences fast-start responses, the primary defensive behaviour in a range of taxa, including fish, sharks, and larval amphibians. We focused on reactivity through response latency and kinematic performance (i.e. agility and propulsion) following a simulated predator attack, while distinguishing between first and subsequent responders (direct response to stimulation versus response triggered by integrated direct and social stimulation, respectively). In familiar schools, first and subsequent responders exhibited shorter latency than unfamiliar individuals, demonstrating that familiarity increases reactivity to direct and, potentially, …

Birds Ruffled By Big-City Lights, Lauren E. Nadler

Marine & Environmental Sciences Faculty Articles

No abstract provided.

A Brain-Infecting Parasite Impacts Host Metabolism Both During Exposure And After Infection Is Established, Lauren E. Nadler, Erik Bengston, Erika J. Eliason, Cameron Hassibi, Siri H. Helland-Riise, Ida B. Johansen, Garfield T. Kwan, Martin Tresguerres, Andrew V. Turner, Kelly L. Weinersmith, Øyvind Øverli, Ryan F. Hechinger

Marine & Environmental Sciences Faculty Datasets

1. Metabolic costs associated with parasites should not be limited to established infections. Even during initial exposure to questing and attacking parasites, hosts can enact behavioural and physiological responses that could also incur metabolic costs. However, few studies have measured these costs directly. Hence, little is known about metabolic costs arising from parasite exposure.
2. Further, no one has yet measured whether and how previous infection history modulates metabolic responses to parasite exposure.
3. Here, using the California killifish (Fundulus parvipinnis) and its brain-infecting parasite (Euhaplorchis californiensis), we quantified how killifish metabolism, behaviour, and osmoregulatory phenotype changed upon acute …

A Brain-Infecting Parasite Impacts Host Metabolism Both During Exposure And After Infection Is Established, Lauren E. Nadler, Erik Bengston, Erika J. Eliason, Cameron Hassibi, Siri H. Helland-Riise, Ida B. Johansen, Garfield T. Kwan, Martin Tresguerres, Andrew V. Turner, Kelly L. Weinersmith, Øyvind Øverli, Ryan F. Hechinger

Marine & Environmental Sciences Faculty Articles

1. Metabolic costs associated with parasites should not be limited to established infections. Even during initial exposure to questing and attacking parasites, hosts can enact behavioural and physiological responses that could also incur metabolic costs. However, few studies have measured these costs directly. Hence, little is known about metabolic costs arising from parasite exposure.
2. Furthermore, no one has yet measured whether and how previous infection history modulates metabolic responses to parasite exposure.
3. Here, using the California killifish Fundulus parvipinnis and its brain‐infecting parasite Euhaplorchis californiensis, we quantified how killifish metabolism, behaviour and osmoregulatory phenotype changed upon acute exposure to parasite …

The Efficacy Of Whole Human Genome Capture On Ancient Dental Calculus And Dentin, Kirsten A. Ziesemer, Jazmin Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-Garcia, Bruno Frohlich, George R. Miller, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis Jr., Corinne L. Hofman, Christina Warinner, Hannes Schroeder

Biology Faculty Articles

Objectives

Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.

Materials and methods

Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing.

Results

Total DNA from calculus exceeded that of dentin in all cases, …

Stable Isotope (13c/15n) Data Of Meso- And Bathypelagic Nekton, Northern Gulf Of Mexico, March - September 2011, T. M. Richards, E. E. Gipson

DEEPEND Datasets

These data represent stable isotope values (13C/15N) of eight species of meso- and bathypelagic nekton collected in the northern Gulf of Mexico during spring (22-March to 11-April), summer (23-June to 13-July), and fall (8-September to 27-September) of 2011. The species examined in this study include: Anoplogaster cornuta, Chauliodus sloani, Coccorella atlantica, Gigantura chuni, Gigantura indica, Omosudis lowii, Photostomias guernei, and Stomias affinis. Isotope values are derived from white muscle tissue dissected from 212 individual fish that were collected using large mid-water trawls towed from the surface to depths of either 700 or 1400 m. The samples were collected as part …

Is There A Link Between Aging And Microbiome Diversity In Exceptional Mammalian Longevity?, Graham M. Hughes, John Leech, Sebastien J. Puechmaille, Jose V. Lopez, Emma C. Teeling

Biology Faculty Articles

A changing microbiome has been linked to biological aging in mice and humans, suggesting a possible role of gut flora in pathogenic aging phenotypes. Many bat species have exceptional longevity given their body size and some can live up to ten times longer than expected with little signs of aging. This study explores the anal microbiome of the exceptionally long-lived Myotis myotis bat, investigating bacterial composition in both adult and juvenile bats to determine if the microbiome changes with age in a wild, long-lived non-model organism, using non-lethal sampling. The anal microbiome was sequenced using metabarcoding in more than 50 …

Cooperation And Competition Shape Ecological Resistance During Periodic Spatial Disturbance Of Engineered Bacteria, Cortney E. Wilson, Allison J. Lopatkin, Travis J. A. Craddock, William W. Driscoll, Omar T. Eldakar, Jose V. Lopez, Robert P. Smith

Biology Faculty Articles

Cooperation is fundamental to the survival of many bacterial species. Previous studies have shown that spatial structure can both promote and suppress cooperation. Most environments where bacteria are found are periodically disturbed, which can affect the spatial structure of the population. Despite the important role that spatial disturbances play in maintaining ecological relationships, it remains unclear as to how periodic spatial disturbances affect bacteria dependent on cooperation for survival. Here, we use bacteria engineered with a strong Allee effect to investigate how the frequency of periodic spatial disturbances affects cooperation. We show that at intermediate frequencies of spatial disturbance, the …

Perspectives Provided By Leopard And Other Cat Genomes: How Diet Determined The Evolutionary History Of Carnivores, Omnivores, And Herbivores, Soonok Kim, Yun Sung Cho, Jong Bhak, Stephen J. O'Brien, Joo-Hong Yeo

Biology Faculty Articles

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found …

Investigating The Spatial Distribution And Effects Of Nearshore Topography On Acropora Cervicornis Abundance In Southeast Florida, Nicole D'Antonio, David S. Gilliam, Brian K. Walker

Marine & Environmental Sciences Faculty Articles

Dense Acropora cervicornis aggregations, or patches, have been documented within nearshore habitats in Southeast Florida (SE FL) despite close proximity to numerous anthropogenic stressors and subjection to frequent natural disturbance events. Limited information has been published concerning the distribution and abundance of A. cervicornis outside of these known dense patches. The first goal of this study was to conduct a spatially extensive and inclusive survey (9.78 km²) to determine whether A. cervicornis distribution in the nearshore habitat of SE FL was spatially uniform or clustered. The second goal was to investigate potential relationships between broad-scale seafloor topography and …