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Full-Text Articles in Biology

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 Dec 2023

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


Recombination As An Enforcement Mechanism Of Prosocial Behavior In Cooperating Bacteria, Isaiah Paolo A. Lee, Omar Tonsi Eldakar, J. Peter Gogarten, Cheryl P. Andam Aug 2023

Recombination As An Enforcement Mechanism Of Prosocial Behavior In Cooperating Bacteria, Isaiah Paolo A. Lee, Omar Tonsi Eldakar, J. Peter Gogarten, Cheryl P. Andam

Biology Faculty Articles

Prosocial behavior is ubiquitous in nature despite the relative fitness costs carried by cooperative individuals. However, the stability of cooperation in populations is fragile and often maintained through enforcement. We propose that homologous recombination provides such a mechanism in bacteria. Using an agent-based model of recombination in bacteria playing a public goods game, we demonstrate how changes in recombination rates affect the proportion of cooperating cells. In our model, recombination converts cells to a different strategy, either freeloading (cheaters) or cooperation, based on the strategies of neighboring cells and recombination rate. Increasing the recombination rate expands the parameter space in …


Periodically Disturbing Biofilms Reduces Expression Of Quorum Sensing-Regulated Virulence Factors In Pseudomonas Aeruginosa, Laura Garcia-Dieguez, Gabriela Diaz-Tang, Estefania Marin Meneses, Vanessa Cruise, Ivana M. Barraza, Travis J.A. Craddock, Robert P. Smith Jun 2023

Periodically Disturbing Biofilms Reduces Expression Of Quorum Sensing-Regulated Virulence Factors In Pseudomonas Aeruginosa, Laura Garcia-Dieguez, Gabriela Diaz-Tang, Estefania Marin Meneses, Vanessa Cruise, Ivana M. Barraza, Travis J.A. Craddock, Robert P. Smith

Biology Faculty Articles

Pseudomonas aeruginosa uses quorum sensing to regulate the expression of virulence factors. In static environments, spatial structures, such as biofilms, can increase the expression of these virulence factors. However, in natural settings, biofilms are exposed to physical forces that disrupt spatial structure, which may affect the expression of virulence factors regulated by quorum sensing. We show that periodically disturbing biofilms composed of P. aeruginosa using a physical force reduces the expression of quorum sensing-regulated virulence factors. At an intermediate disturbance frequency, the expression of virulence factors in the las, rhl, and pqs regulons is reduced. Mathematical modeling suggests that perturbation …


Variability In Billfish Vertical Distribution And Fishing Interactions Driven By Environmental Conditions In The Eastern Tropical Pacific Ocean, H. E. Blondin, D. E. Haulsee, Ryan Logan, Mahmood Shivji, E. R. Hoffmayer, J. H. Walker, J. M. Dean, E. L. Hazen, L. B. Crowder Jun 2023

Variability In Billfish Vertical Distribution And Fishing Interactions Driven By Environmental Conditions In The Eastern Tropical Pacific Ocean, H. E. Blondin, D. E. Haulsee, Ryan Logan, Mahmood Shivji, E. R. Hoffmayer, J. H. Walker, J. M. Dean, E. L. Hazen, L. B. Crowder

Biology Faculty Articles

Blue marlin (Makaira nigricans) and sailfish (Istiophorus platypterus) are ecologically important predators and valuable species throughout the world’s recreational, commercial, and subsistence fisheries. Comparing multi-species vertical habitat use can inform ecological uncertainties such as inter-species competition, as well as relative vulnerabilities to fishing activities. In this study, we identified key differences in both depth use and which environmental variables drive these selections, which highlights the variability in the catchability both as target species in recreational fisheries and bycatch in commercial fisheries. To understand these two species’ vertical habitat use, we examined depth profiles from 26 sailfish …


Patrolling The Border: Billfish Exploit The Hypoxic Boundary Created By The World's Largest Oxygen Minimum Zone, Ryan Logan, Jeremy J. Vaudo, Brad Wetherbee, Mahmood Shivji Jun 2023

Patrolling The Border: Billfish Exploit The Hypoxic Boundary Created By The World's Largest Oxygen Minimum Zone, Ryan Logan, Jeremy J. Vaudo, Brad Wetherbee, Mahmood Shivji

Biology Faculty Articles

Pelagic predators must contend with low prey densities that are irregularly distributed and dynamic in space and time. Based on satellite imagery and telemetry data, many pelagic predators will concentrate horizontal movements on ephemeral surface fronts—gradients between water masses—because of enhanced local productivity and increased forage fish densities.
Vertical fronts (e.g. thermoclines, oxyclines) can be spatially and temporally persistent, and aggregate lower trophic level and diel vertically migrating organisms due to sharp changes in temperature, water density or available oxygen. Thus, vertical fronts represent a stable and potentially energy rich habitat feature for diving pelagic predators but remain little explored …


Potential Impacts Of Environmental Bacteria On The Microbiota Of Loggerhead (Caretta Caretta) And Green (Chelonia Mydas) Sea Turtle Eggs And Their Hatching Success, Colleen Mcmaken, Derek Burkholder, Rosanna J. Milligan Dr., Jose V. Lopez Jun 2023

Potential Impacts Of Environmental Bacteria On The Microbiota Of Loggerhead (Caretta Caretta) And Green (Chelonia Mydas) Sea Turtle Eggs And Their Hatching Success, Colleen Mcmaken, Derek Burkholder, Rosanna J. Milligan Dr., Jose V. Lopez

Biology Faculty Articles

Sea turtle hatching success can be affected by many variables, including pathogenic microbes, but it is unclear which microbes are most impactful and how they are transmitted into the eggs. This study characterized and compared the bacterial communities from the (i) cloaca of nesting sea turtles (ii) sand within and surrounding the nests; and (iii) hatched and unhatched eggshells from loggerhead (Caretta caretta) and green (Chelonia mydas) turtles. High throughput sequencing of bacterial 16S ribosomal RNA gene V4 region amplicons was performed on samples collected from 27 total nests in Fort Lauderdale and Hillsboro beaches in …


Interactions Between Metabolism And Growth Can Determine The Co-Existence Of Staphylococcus Aureus And Pseudomonas Aeruginosa, Camryn Pajon, Marla C. Fortoul, Gabriela Diaz-Tang, Estefania Marin Meneses, Ariane R. Kalifa, Elinor Sevy, Taniya Mariah, Brandon Toscan, Maili Marcelin, Daniella M. Hernandez, Melissa M. Marzouk, Allison J. Lopatkin, Omar T. Eldakar, Robert Smith Apr 2023

Interactions Between Metabolism And Growth Can Determine The Co-Existence Of Staphylococcus Aureus And Pseudomonas Aeruginosa, Camryn Pajon, Marla C. Fortoul, Gabriela Diaz-Tang, Estefania Marin Meneses, Ariane R. Kalifa, Elinor Sevy, Taniya Mariah, Brandon Toscan, Maili Marcelin, Daniella M. Hernandez, Melissa M. Marzouk, Allison J. Lopatkin, Omar T. Eldakar, Robert Smith

Biology Faculty Articles

Most bacteria exist and interact within polymicrobial communities. These interactions produce unique compounds, increase virulence and augment antibiotic resistance. One community associated with negative healthcare outcomes consists of Pseudomonas aeruginosa and Staphylococcus aureus. When co-cultured, virulence factors secreted by P. aeruginosa reduce metabolism and growth in S. aureus. When grown in vitro, this allows P. aeruginosa to drive S. aureus toward extinction. However, when found in vivo, both species can co-exist. Previous work has noted that this may be due to altered gene expression or mutations. However, little is known about how the growth environment could influence the …


Decontamination And Annotation Of The Draft Genome Sequence Of The Oomycete Lagenidium Giganteum Arsef 373, William R. Morgan, Aurelien Tartar Apr 2023

Decontamination And Annotation Of The Draft Genome Sequence Of The Oomycete Lagenidium Giganteum Arsef 373, William R. Morgan, Aurelien Tartar

Biology Faculty Articles

Scaffolds of a previously published Lagenidium giganteum ARSEF 373 genome assembly found at GenBank were filtered to remove contaminating sequences. Genome annotation of the 437 scaffolds (total length, 56.2 MB; GC content, 58.8%) with confirmed L. giganteum sequences identified 13,069 potential protein-coding genes, encoding at least 737 predicted secreted proteins and .100 putative translocated effectors


Acoustic Telemetry Provides Insights For Improving Conservation And Management At A Spawning Aggregation Site Of The Endangered Nassau Grouper (Epinephelus Striatus), Richard S. Nemeth, Elizabeth Kadison, Jonathan Jossart, Mahmood Shivji, Bradley Wetherbee, Jordan Matley Mar 2023

Acoustic Telemetry Provides Insights For Improving Conservation And Management At A Spawning Aggregation Site Of The Endangered Nassau Grouper (Epinephelus Striatus), Richard S. Nemeth, Elizabeth Kadison, Jonathan Jossart, Mahmood Shivji, Bradley Wetherbee, Jordan Matley

Biology Faculty Articles

Nassau grouper (Epinephelus striatus, Serranidae) were one of the most important fishery species in the Caribbean, but are now listed as critically endangered. Population collapse in most places occurred primarily by fishers targeting their spawning aggregation sites, where thousands of fish gathered during full moon periods from December to April. Identifying management options for protecting this vulnerable period is crucial for their survival. In the US Virgin Islands, we tagged 24 Nassau grouper with acoustic transmitters at a fish spawning aggregation (FSA) site called the Grammanik Bank, a 1.5 km2, marine protected area (MPA) closed each year from …


Morphological And Transcriptional Effects Of Crude Oil And Dispersant Exposure On The Marine Sponge Cinachyrella Alloclada, Yvain Desplat, Jacob F. Warner, Emily J. Blake, Nidhi Vijayan, Marie Cuvelier, Patricia Blackwelder, Jose V. Lopez Mar 2023

Morphological And Transcriptional Effects Of Crude Oil And Dispersant Exposure On The Marine Sponge Cinachyrella Alloclada, Yvain Desplat, Jacob F. Warner, Emily J. Blake, Nidhi Vijayan, Marie Cuvelier, Patricia Blackwelder, Jose V. Lopez

Biology Faculty Articles

Marine sponges play important roles in benthic ecosystems. More than providing shelter and food to other species, they help maintain water quality by regulating nitrogen and ammonium levels in the water, and bioaccumulate heavy metals. This system, however, is particularly sensitive to sudden environmental changes including catastrophic pollution event such as oil spills. Hundreds of oil platforms are currently actively extracting oil and gas in the Gulf of Mexico. To test the vulnerability of the benthic ecosystems to oil spills, we utilized the Caribbean reef sponge, Cinachyrella alloclada, as a novel experimental indicator. We have exposed organisms to crude …


Chromosome-Length Assembly Of The Baikal Seal (Pusa Sibirica) Genome Reveals A Historically Large Population Prior To Isolation In Lake Baikal, Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta R. Beklemisheva, Maria Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalya A. Serdyukova, Michael Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla L. Lapidus, Dna Zoo Consortium, Stephen James O'Brien, Alexander S. Graphodatsky, Klaus-Peter Koepfli, Sergey Kliver Feb 2023

Chromosome-Length Assembly Of The Baikal Seal (Pusa Sibirica) Genome Reveals A Historically Large Population Prior To Isolation In Lake Baikal, Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta R. Beklemisheva, Maria Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalya A. Serdyukova, Michael Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla L. Lapidus, Dna Zoo Consortium, Stephen James O'Brien, Alexander S. Graphodatsky, Klaus-Peter Koepfli, Sergey Kliver

Biology Faculty Articles

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied …


Dysregulation Of Mir-155 Expression In Professional Mixed Martial Arts (Mma) Fighters, Dominick Cabrera, Kayla Thompson, Julius D. Thomas, Corey Peacock, Jose Antonio, Jaime Tartar, Aurelien Tartar Feb 2023

Dysregulation Of Mir-155 Expression In Professional Mixed Martial Arts (Mma) Fighters, Dominick Cabrera, Kayla Thompson, Julius D. Thomas, Corey Peacock, Jose Antonio, Jaime Tartar, Aurelien Tartar

Biology Faculty Articles

Psychological and physical stress can induce dysregulation of gene expression via changes in DNA methylation and microRNA (miRNA) expression. Such epigenetic modifications are yet to be investigated in professional Mixed Martial Arts (MMA) fighters subject to highly stressful training involving repetitive head impacts. This study examined differences in DNA methylation and miRNA expression in elite MMA fighters compared to active controls. Global methylation differences between groups were assessed via a LINE-1 assay. At the same time, PCR arrays were used to estimate differential expression in samples of 21 fighters and 15 controls for 192 different miRNAs associated with inflammatory diseases. …


Population Structure And Hybridisation In A Population Of Hawaiian Feral Chickens, Maria Luisa Martin Cerezo, Saioa Lopez, Lucy Van Dorp, Garrett Hellenthal, Martin Johnsson, Eben Gering, Rie Henriksen, Dominic Wright Feb 2023

Population Structure And Hybridisation In A Population Of Hawaiian Feral Chickens, Maria Luisa Martin Cerezo, Saioa Lopez, Lucy Van Dorp, Garrett Hellenthal, Martin Johnsson, Eben Gering, Rie Henriksen, Dominic Wright

Biology Faculty Articles

Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976–1995), coinciding …


Hunting Behavior Of A Solitary Sailfish Istiophorus Platypterus And Estimated Energy Gain After Prey Capture, Ryan K. Logan, Sarah M. Luongo, Jeremy Vaudo, Bradley M. Wetherbee, Mahmood Shivji Jan 2023

Hunting Behavior Of A Solitary Sailfish Istiophorus Platypterus And Estimated Energy Gain After Prey Capture, Ryan K. Logan, Sarah M. Luongo, Jeremy Vaudo, Bradley M. Wetherbee, Mahmood Shivji

Biology Faculty Articles

Foraging behavior and interaction with prey is an integral component of the ecological niche of predators but is inherently difficult to observe for highly mobile animals in the marine environment. Billfishes have been described as energy speculators, expending a large amount of energy foraging, expecting to offset high costs with periodic high energetic gain. Surface-based group feeding of sailfish, Istiophorus platypterus, is commonly observed, yet sailfish are believed to be largely solitary roaming predators with high metabolic requirements, suggesting that individual foraging also represents a major component of predator–prey interactions. Here, we use biologging data and video to examine daily …


Genomes Of Endangered Great Hammerhead And Shortfin Mako Sharks Reveal Historic Population Declines And High Levels Of Inbreeding In Great Hammerhead, Michael J. Stanhope, Kristina M. Ceres, Qi Sun, Minghui Wang, Jordan D. Zehr, Nicholas J. Marra, Aryn P. Wilder, Cheng Zou, Andrea M. Bernard, Paulina D. Pavinski Bitar, Mitchell G. Lokey, Mahmood Shivji Jan 2023

Genomes Of Endangered Great Hammerhead And Shortfin Mako Sharks Reveal Historic Population Declines And High Levels Of Inbreeding In Great Hammerhead, Michael J. Stanhope, Kristina M. Ceres, Qi Sun, Minghui Wang, Jordan D. Zehr, Nicholas J. Marra, Aryn P. Wilder, Cheng Zou, Andrea M. Bernard, Paulina D. Pavinski Bitar, Mitchell G. Lokey, Mahmood Shivji

Biology Faculty Articles

Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and 1 Mbp. Both these sharks experienced precipitous declines in …


Change And Stasis Of Distinct Sediment Microbiomes Across Port Everglades Inlet (Pei) And The Adjacent Coral Reefs, Lauren E. Krausfeldt, Jose V. Lopez, Catherine Bilodeau, Hyo Won Lee, Shelby L. Casali Jan 2023

Change And Stasis Of Distinct Sediment Microbiomes Across Port Everglades Inlet (Pei) And The Adjacent Coral Reefs, Lauren E. Krausfeldt, Jose V. Lopez, Catherine Bilodeau, Hyo Won Lee, Shelby L. Casali

Biology Faculty Articles

Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S …


Immersive Learning And Participatory Engagement: Connecting In The Online Classroom Through Virtual Reality, Gesulla Cavanaugh, Helen M. Condry, Clarissa Frances Afable, Melissa Morris, Santanu De, Holly Evans Madison, Jacqueline Marshall, Chitra Paul Victor, Marsha Weiner Jan 2023

Immersive Learning And Participatory Engagement: Connecting In The Online Classroom Through Virtual Reality, Gesulla Cavanaugh, Helen M. Condry, Clarissa Frances Afable, Melissa Morris, Santanu De, Holly Evans Madison, Jacqueline Marshall, Chitra Paul Victor, Marsha Weiner

Biology Faculty Articles

Guided by constructivist theory, this study examines health professions student learning and engagement in the virtual classroom (VC) setting. Students (N=52) participated in a one-week VC prior to and during the COVID-19 pandemic. After participation, students were surveyed to discern their impressions of the experience, including the administration of a presence questionnaire, a key indicator of virtual environment (VE) efficacy. High student presence scores were significantly correlated with the perception that the VC facilitated learning (r = .573, p = .001). Conversely, students who perceived the course content as challenging were less likely to recommend the VC as a viable …