INTEGRATIVE BIOLOGY THURSDAY SEMINAR SERIES
The IB Seminar Series will be held in the CAS Multidisciplinary Complex (CMC 147), 3:30PM on Thursdays. (CMC is along Leroy Collins Blvd, parking lot 2A/B, near BSF) MAP
ONLINE 2015 FALL WORKSHOP IN DATA ANALYSIS VIDEOS
In October 2015, the Department of Integrative Biology, working with the College of Arts and Science, ResearchOne, and the Interdisciplinary Data Sciences Consortium, offered a set of workshops on data analysis. Two of the lectures from the workshop are available (below) as online videos.
- Introduction to spatial linear models; Spatial linear models in R, by Simoneta Negrete Yankelevich, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico. Spatial phenomena are important in many kinds of data, especially environmental data. This is an introduction to spatial linear models, a central set of tools for assessing spatial phenomena and beginning to quantify them. It is based on the chapter on this topic in Fox, Negrete, and Sosa (eds). 2015. Ecological statistics: contemporary theory and application. Oxford University Press. The workshop was given at the University of South Florida.
- Introduction to analysis of censored and truncated data, by Gordon Fox, USF Integrative Biology. Data in many settings are censored: we know only an inequality about some values - for example, that a particular value weighs less than the scale permits. In other settings, data are truncated: we aren't even recording the existence of certain types of values. There are some well-developed methods for analyzing these data; this is an introduction. It uses the chapter on this topic in Fox, Negrete, and Sosa, eds. (2015). Ecological statistics: contemporary theory and application. Oxford University Press.
Gordon Fox was featured in an interview on WMNF Public Radio (88.5 FM, Tampa, Florida) on the effects of climate change on the spread of diseases around the world. He pointed out that the recent outbreak of the Zika virus is not the only pathogen spreading in Florida, that the state is also falling victim to the Texas Phoenix Palm Decline , which is infecting trees including date palms and cabbage palms in Florida. Tampa is the center of the outbreak in the state. The disease is caused by a bacteria which was imported into the state with infected plants. Gordon discusses the problem with world travel and human interest in novel plants and animals introducing new species to new parts of the globe. These new species carry new diseases with them. Read his interview, or listen to it, at the WMNF RADIO site.
Tom and Beverly Porter continue to support USF Integrative Biology and Dr. Motta's lab since their daughter, Heather, graduated in 1997. Their donations to USF have helped Department of Integrative Biology students in the lab of Dr. Philip Motta, studying the feeding behavior of sharks, tagging sharks aboard a research vessel, taking field trips to the Florida Keys reefs to study fishes and in one-on-one mentoring, and in the lab of Dr. Stephen Deban, using high speed videography to compare feeding patterns of different salamander species. These are just a few of the valuable research opportunities USF's Integrative Biology students have taken part in. Learn more about the story, and the research opportunities in Integrative Biology in the following video:
The USF Faculty Senate Honors and Awards Council has concluded its deliberations for the 2016 Spring Semester, and selected Dr. Jason Rohr, (USF Integrative Biology), to receive the 2016 Jerome Krivanek Distinguished Teacher Award. The award will be presented later this year by the Provost’s office. Jason began his teaching career as an Assistant Professor in the USF Biology Department in 2007, and is currently an Associate Professor, teaching classes in the Department of Integrative Biology on parasitology, animal behavior, and graduate-level introductory and advanced biological statistics. He was recently appointed Director of the Center for Infectious Disease Ecology Research (CIDER), a newly formed research center at USF, to which the Department of Integrative Biology is affiliated. His world-renowned research includes studies on ecotoxicity of pesticides and herbicides, chytrid fungal effects on amphibians, and anthropogenic changes to ecosystems. Congratulations on your award!
USF and the Florida Board of Governors met recently to officially approve the establishment of a Center for Infectious Disease Ecology Research (CIDER) on campus. The Center will be affiliated with the USF Department of Integrative Biology. The purpose of the Center is to bring together researchers on campus that are interested in diseases ecology. It will also facilitate in the training of disease ecologists and attract new disease ecologist faculty to USF. Disease ecology is the interaction of the behavior and ecology of hosts with the biology of pathogens, as it relates to the impact of diseases on populations.
CHANTALE BÉGIN AND CHRISTOPHER OSOVITZ
The USF Transformation Implementation Leadership Team (TILT) has recommended for implementation and will provide support for proposals submitted to the team by two USF Integrative Biology faculty members, Chantale Bégin and Christopher Osovitz. Chantale joined Vasala Mohanakumar from Hillsborough Community College in submitting a proposal titled “Transforming STEM Education at USF and HCC”, while Chris joined an eight-member team that also included faculty from the USF Departments of CMMB, Chemistry, and Mathematics and faculty from HCC in submitting a proposal titled “Mathematics Foundation for Sciences”. Project STEER (Systemic Transformation of Education through Evidence-Based Reforms) is a program supported largely by a $3M NSF IUSE grant to a broadly representative USF team to develop an institutional culture that improves the retention rate and preparation of students who enter USF as STEM majors. STEER has a special focus on underrepresented groups. On January 30, STEER held an interdisciplinary retreat. One of the outcomes of the retreat was an invitation to faculty to submit course redesign proposals with support of STEER. Each proposed project was expected to enhance curricular alignment and adoption of evidence-based strategies, strategies that have been validated by extensive research to be effective in reaching the overall national goal. Chantale and Chris submitted proposals expected to reach these goals. TILT members will serve as advisors and consultants in the development of work plans to implement the proposals. The funding provided in the awards is in recognition of the additional effort the participating faculty will have to expend on these projects. Congratulations on your awards!
THOMAS CRISMAN AT STATE DEPARTMENT
Dr. Thomas Crisman, joint professor in USF Integrative Biology and the College of Public Health’s Department of Environmental and Occupational Health, recently concluded an a one year fellowship with the U.S. Department of State and USAID’s Jefferson Science Fellowship Program. He was one of 13 fellows chosen nationally to offer their insight on bridging science and U.S. policy. Working in the Office of Conservation and Water, Crisman led an expert group working to help with revisions of the environmental safeguards that the World Bank applies to all loans. He was also responsible for reviewing environmental assessment for large dams globally prior to World Bank funding approval. “I would give the State Department’s view before sending it to the Treasury for submittal to the World Bank,” Crisman said. He also helped set up a new program bringing together religious values of local people and water usage, taking into account local social values associated with water management. He started his efforts on the Balkans and will continue on to Albania, Macedonia and Croatia. Although his Jefferson Science fellowship has concluded, he is still continuing his work with the U.S. Department of the State as a Jefferson Science Fellow. In addition to this, Crisman has served for the past 20 years on the board of the United States–Israel Binational Science Foundation as one of five Americans responsible for overseeing the distribution of U.S.-Israeli funding for cooperative science between the two nations. He has also served as a consultant for numerous U.S. embassies around the world on water management issues. More of his story is featured in a story at USF College of Public Health News.
The new fields of ecological immunology and disease ecology have begun to merge, and the classic fields of immunology and epidemiology are beginning to blend with them. This merger is occurring because the integrative study of host–parasite interactions is providing insights into disease in ways that traditional methods have not. With the advent of new tools, mathematical and technological, scientists could be on the verge of developing a unified theory of infectious disease, one that supersedes the barriers of jargon and tradition. Authors Lynn (Marty) Martin, (USF Integrative Biology), Sarah Burgan, (USF Integrative Biology), James Adelman, (Virginia Tech, Blackburg, VA.), and Stephanie Gervasi, (Monell Chemical Senses Center, Philadelphia, PA.) argue that a cornerstone of any such synthesis will be PRNSHOST, the propensity of an individual host to generate new infections in other susceptible hosts. In the last few years, the emergence of systems immunology has led to novel insight into how hosts control or eliminate pathogens. Most such efforts have stopped short of considering transmission and the requisite behaviors of infected individuals that mediate it, and few have explicitly incorporated ecological and evolutionary principles. Ultimately though, scientists expect that the use of a systems immunology perspective will help link suborganismal processes (i.e., health of hosts and selection on genes) to superorganismal outcomes (i.e., community-level disease dynamics and host–parasite coevolution). Recently, physiological regulatory networks (PRNs) were cast as whole-organism regulatory systems that mediate homeostasis and hence link suborganismal processes with the fitness of individuals. The authors use the PRN construct to develop a roadmap for studying host competence, taking guidance from systems immunology and evolutionary ecology research. They argue that PRN variation underlies heterogeneity in individual host competence and hence host–parasite dynamics. Their study is published in the journal Integrative and Comparative Biology.
Microbial source tracking (MST) endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. In a review paper, authors Warish Ahmed, (CSIRO Land and Water, Brisbane, Queensland, AU), Bridie Hughes, (CSIRO Land and Water, Brisbane, Queensland, AU), and Valerie (Jody) Harwood, (USF Integrative Biology) summarize the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or “markers” of sewage pollution, including known advantages and deficiencies of the many polymerase chain reaction (PCR)-based methods that have been published since 2000. Host specificity is a paramount criterion for confidence that detection of a marker is a true indicator of the target host. Host sensitivity, or the prevalence of the marker in feces/waste from the target host, is necessary for confidence that absence of the marker is indicative of the absence of the pollution source. Each of these parameters can vary widely depending on the type of waste assessed and the geographic location. Differential decay characteristics of bacterial targets and their associated DNA contribute to challenges in interpreting MST results in the context of human health risks. The HF183 marker, derived from the 16S rRNA gene of Bacteroides dorei and closely related taxa, has been used for almost two decades in MST studies, and is well characterized regarding host sensitivity and specificity, and in prevalence and concentration in sewage in many countries. Other markers such as HumM2 and HumM3 show promise, but require further performance testing to demonstrate their widespread utility. An important limitation of the one-marker-one-assay approach commonly used for MST is that given the complexities of microbial persistence in environmental waters, and the methodological challenges of quantitative PCR (qPCR) in such samples, the absence of a given marker does not ensure the absence of fecal pollution in the source water. Approaches under development, such as microarray and community analysis, have the potential to improve MST practices, thereby increasing our ability to protect human and ecosystem health. Their study is published in the journal Water.
Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Authors Jason Rohr, (USF Integrative Biology), Christopher Salice, (Towson Univ., Towson, MD.), and Roger Nisbet, (Univ. of California Santa Barbara, Santa Barbara, CA.) reviewed the pros and cons of ERA across levels of biological organization, including suborganismal (e.g., biomarkers), individual, population, community, ecosystem and landscapes levels. Their review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, the authors also reviewed mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, they provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing mathematical modeling approaches where possible to enhance ERA. Because top-down ERA is unconventional, they also offer some suggestions for how it might be implemented efficaciously. The authors state that they hope this review helps researchers in the field of ERA fill key information gaps and helps risk assessors identify the best levels of biological organization to conduct ERAs with differing goals. Their paper is published in the journal Critical Reviews in Toxicology.
In a previous paper (Blood-brain barrier alterations provide evidence of subacute diaschisis in an ischemic stroke rat model, PLoS ONE), authors Svitlana Garbuzova-Davis, (Center of Excellence for Aging and Brain Repair, Morsani College of Medicine, Univ. of South Florida, Tampa, Fl.), Edward Haller, (USF Integrative Biology), Naoki Tajiri, (CEABR, USF), Avery Thomson, (CEABR, USF), Jennifer Barretta, (CEABR, USF), Stephanie Williams, (CEABR, USF), Eithan Haim, (CEABR, USF), Hua Qin, (CEABR, USF), Aric Frisina-Deyo, (CEABR, USF), Jerry Abraham, (CEABR, USF), Paul Sanberg, (CEABR, USF), Harry Van Loveren, (Dept. of Neurosurgery and Brain Repair, Morsani C. of M., USF), and Cesario V. Borlongan, (CEABR, USF) demonstrated blood-brain barrier impairment in remote contralateral brain areas in rats at 7 and 30 days after transient middle cerebral artery occlusion (tMCAO), indicating ischemic diaschisis. Their current study focused on effects of subacute and chronic focal cerebral ischemia on the blood-spinal cord barrier (BSCB). They observed BSCB damage on both sides of the cervical spinal cord in rats at 7 and 30 days post-tMCAO. Major BSCB ultrastructural changes in spinal cord gray and white matter included vacuolated endothelial cells containing autophagosomes, pericyte degeneration with enlarged mitochondria, astrocyte end-feet degeneration and perivascular edema; damaged motor neurons, swollen axons with unraveled myelin in ascending and descending tracts and astrogliosis were also observed. Evans Blue dye extravasation was maximal at 7 days. There was immunofluorescence evidence of reduction of microvascular expression of tight junction occludin, upregulation of Beclin-1 and LC3B immunoreactivities at 7 days and a reduction of the latter at 30 days post-ischemia. These novel pathological alterations on the cervical spinal cord microvasculature in rats after tMCAO suggest pervasive and long-lasting BSCB damage after focal cerebral ischemia, and that spinal cord ischemic diaschisis should be considered in the pathophysiology and therapeutic approaches in patients with ischemic cerebral infarction. Their current study is published in the Oxford Journal of Neuropathology and Experimental Neurology. The story of their research is featured in an article in ScienceDaily.
Muscle-powered movements are limited by the contractile properties of muscles and are sensitive to temperature changes. Elastic-recoil mechanisms can both increase performance and mitigate the effects of temperature on performance. Authors Jeffrey Scales, Charlotte Stinson and Stephen Deban, (USF Integrative Biology, Deban lab) compared feeding movements in two species of plethodontid salamanders, Bolitoglossa franklini and Desmognathus quadramaculatus, across a range of body temperatures (5-25°C) to better understand the mechanism of elastically powered, thermally robust movements. Bolitoglossa exhibited ballistic, elastically powered tongue projection with a maximum muscle mass specific power of 4,642 W kg -1 while Desmognathus demonstrated nonballistic, muscle-powered tongue projection with a maximum power of 359 W kg -1. Tongue-projection performance in Bolitoglossa was more thermally robust than that of Desmognathus, especially below 15°C. The improved performance and thermal robustness of Bolitoglossa was associated with morphological changes in the projector muscle, including elaborated collagen aponeuroses and the absence of myofibers attaching directly to the tongue skeleton. The elongated aponeuroses likely increase the capacity for elastic energy storage, and the lack of myofibers inserting on the tongue skeleton permits ballistic projection. These results suggest that relatively simple changes in myofiber architecture and the amount of connective tissue can improve the performance and functional robustness of movements in the face of environmental challenges such as variable temperature. Their study is published in the Journal of Experimental Zoology Part A Ecological Genetics and Physiology.
Brad Gemmell studies the methods of locomotion of various marine organisms, from plankton to siphonophores to jellyfish to lampreys. In a recent study on moon jellyfish, Aurelia aurita, Brad and his research associates discovered that the jellies, which must constantly keep swimming night and day, are more efficient than any other swimmers, using 48 percent less oxygen than any other animal to move. Their study found that the jellies produce highly efficient regions of high and low pressure around their domes as they contract and expand, sucking and pushing themselves forward in the water. Read the Scientific American Online article here for more interesting information on the jellies, and the original research published in Nature Communications in 2015 here.
The extent to which Marine Protected Areas (MPAs) benefit corals is contentious. On one hand, MPAs could enhance coral growth and survival through increases in herbivory within their borders; on the other, they are unlikely to prevent disturbances, such as terrestrial run-off, that originate outside their boundaries. Authors Chantale Bégin , (USF Integrative Biology), Christiane Schelten, (GEOMAR, Helmholtz Centre for Ocean Research, DE), Maggy Nugues, (Laboratoire d′Excellence ′CORAIL′, Perpignan Cedex, FR), Julie Hawkins, (Univ. of York, Heslington, UK), Callum Roberts, (Univ. of York, Heslington, UK), and Isabelle Côté, (Simon Fraser Univ., Burnaby, BC, CA) examined the effect of spatial protection and terrestrial sediment on the benthic composition of coral reefs in Saint Lucia. In 2011 (10 to 16 years after MPAs were created), the authors resurveyed 21 reefs that had been surveyed in 2001 and analyzed current benthic assemblages as well as changes in benthic cover over that decade in relation to protection status, terrestrial sediment influence (measured as the pro-portion of terrigenous material in reef-associated sediment) and depth. The cover of all benthic biotic components has changed significantly over the decade, including a decline in coral and increase in macroalgae. Protection status was not a significant predictor of either current benthic composition or changes in composition, but current cover and change in cover of several components were related to terrigenous content of sediment deposited recently. Sites with a higher proportion of terrigenous sediment had lower current coral cover, higher macroalgal cover and greater coral declines. Their results suggest that terrestrial sediment is an important factor in the recent degradation of coral reefs in Saint Lucia and that the current MPA network should be complemented by measures to reduce runoff from land. Their work is published in the journal PlosOne
Birds often face various stressors during feather renewing, for example, enduring infection with blood parasites. Because nutritional resources are typically limited, especially for wild animals, when an individual allocates energy to one physiological system, there is subsequently less for other processes, thereby requiring a trade-off. Potential trade-offs between malaria infection and feather growth rate have not been experimentally considered yet. Authors Courtney Coon, (Univ. of Pretoria, Onderstepoort, ZA), Luz Garcia-Longoria, (Univ. of Extremadura, Avda. De Elvas, ES), Lynn (Marty) Martin, (USF Integrative Biology), Sergio Magallanes, (Univ. of Extremadura, Avda. De Elvas, ES), Florentino de Lope, (Univ. of Extremadura, Avda. De Elvas, ES), and Alfonso Marzal, (Univ. of Extremadura, Avda. De Elvas, ES) conducted three studies to investigate whether a trade-off occurs among feather growth rate, malaria infection and host health conditions. First, they explored whether naturally infected and uninfected house sparrows differed in feather growth rate in the wild. Second, they asked whether experimental inoculation of malaria parasites and / or forcing the renewal of a tail feather. Finally, the authors evaluated whether individual condition was affected by experimentally-induced feather regrowth and / or malaria experimental infection. Their findings showed that feather growth rate was negatively affected by natural malaria infection status in free-living birds and by experimental infection in captive birds. Furthermore, birds that did not increase body mass or hematocrit during the experimental study had slower feather growth. Together these results suggest that infection with blood parasites has more negative health effects than the growth of tail feathers and that these two processes (response to blood parasite infection and renewal of feathers) are traded-off against each other. As such, their results highlight the role of malaria parasites as a potential mechanism driving other trade-offs in wild passerines. Their study is published in the Journal of Avian Biology.
Foraging modalities (e.g., passive, sit-and-wait, active) and traits are plastic in some species, but the extent to which this plasticity affects interspecific competition remains unclear. Using a long-term laboratory mesocosm experiment, authors David Jennings, (Univ. of Maryland, College Park, MD), James Krupa, (Univ. of Kentucky, Lexington, KY), and Jason Rohr, (USF Integrative Biology) quantified competition strength and the plasticity of foraging traits in a guild of generalist predators of arthropods with a range of foraging modalities. Each mesocosm contained eight passively foraging pink sundews, and they employed an experimental design where treatments were the presence or absence of a sit-and-wait foraging spider and actively foraging toad crossed with five levels of prey abundance. The authors hypothesized that actively foraging toads would outcompete the other species at low prey abundance, but that spiders and sundews would exhibit plasticity in foraging traits to compensate for strong competition when prey were limited. Results generally supported their hypotheses. Toads had a greater effect on sundews at low prey abundances, and toad presence caused spiders to locate webs higher above the ground. Additionally, the closer large spider webs were to the ground, the greater the trichome densities produced by sundews. Also, spider webs were larger in the presence of than without toads and as sundew numbers increased, and these effects were more prominent as resources became limited. Finally, spiders negatively affected toad growth only at low prey abundance. These findings highlight the long-term importance of foraging modality and plasticity of foraging traits in determining the strength of competition within and across taxonomic kingdoms. Future research should assess whether plasticity in foraging traits helps to maintain coexistence within this guild and whether foraging modality can be used as a trait to reliably predict the strength of competitive interactions. Their study is published in the Journal of Animal Ecology.
A study on the feeding performance of king mackerel, conducted by researchers in the Department of Integrative Biology and the University of Tampa, found its way into an article on sports fishing for king mackerel in Florida Sportsman magazine recently. The research work, “Feeding Performance of King Mackerel, Scomberomorus cavalla”, published in 2015 in the Journal of Experimental Zoology (Amber Ferguson, (USF Integrative Biology graduate, 2014), Daniel Huber, (Univ. of Tampa), Marc Lajeunesse, (USF Integrative Biology) and Philip Motta, (USF Integrative Biology), authors), was a comparative study of the feeding performance of king mackerel, including bite force and feeding mechanism. The mackerel bite force was compared to that of other bony fish and to sharks, with the conclusion that king mackerel rely on high speed impact of their teeth on prey fish to exert bite pressure, in contrast to sharks and fish with large jaw muscles which can generate high bite strength. The April 2016 Florida Sportsman article, titled “The Cutting Edge: What makes the kingfish such a deadly predator also makes it a fisherman’s favorite” features an interview with Philip Motta, one of the Experimental Zoology article co-authors. The Sportsman article quotes from the Zoology paper: “King mackerel, Scomberomorus cavalla, have relatively low performance for bite force compared with other fishes and relatively little of the forward predator force is experienced by the prey.” “However, king mackerel can attain high speeds to chase prey and use sharp teeth to impart high bite pressure, factors which apparently alleviate the need for high bite force.” Phil explains the mackerel feeding research in the article. Read the Experimental Zoology paper here and the Florida Sportsman article here.
Animal behaviour and the ecology and evolution of parasites are inextricably linked. For this reason, animal behaviorists and disease ecologists have been interested in the intersection of their respective fields for decades. Despite this interest, most research at the behaviour–disease interface focuses either on how host behaviour affects parasites or how parasites affect behaviour, with little overlap between the two. Yet, the majority of interactions between hosts and parasites are probably reciprocal, such that host behaviour feeds back on parasites and vice versa. Explicitly considering these feedbacks is essential for understanding the complex connections between animal behaviour and parasite ecology and evolution. Authors Vanessa Ezenwa, (Univ. of Georgia, Athens, GA), Elizabeth Archie, (Univ. of Notre Dame, Notre Dame, IN), Meggan Craft, (Univ. of Minnesota, St. Paul, MN), Lynn (Marty) Martin, (USF Integrative Biology), Janice Moore, (Colorado State Univ., Ft. Collins, CO) and Lauren White, (Univ. of Minnesota, St. Paul, MN) discuss how host behaviour–parasite feedbacks might operate and explore the consequences of feedback for studies of animal behaviour and parasites. For example, ignoring the feedback of host social structure on parasite dynamics can limit the accuracy of predictions about parasite spread. Likewise, considering feedback in studies of parasites and animal personalities may provide unique insight about the maintenance of variation in personality types. Finally, applying the feedback concept to links between host behaviour and beneficial, rather than pathogenic, microbes may shed new light on transitions between mutualism and parasitism. More generally, accounting for host behaviour–parasite feed-backs can help identify critical gaps in our understanding of how key host behaviors and parasite traits evolve and are maintained. Their review article is published in the Proceedings of the Royal Society B.
The factors driving the dominance of the Calvin–Benson–Bassham cycle (CBB) or reductive citric acid cycle (rCAC) in autotrophic microorganisms in different habitats are debated. Based on costs for synthesizing a few metabolic intermediates, it has been suggested that the CBB poses a disadvantage due to higher metabolic cost. Mary Mangiapia and Kathleen (KT) Scott, (USF Integrative Biology) conducted a study to extend the estimate of cost from metabolite synthesis to biomass synthesis. For 12 gammaproteobacteria (CBB) and five epsilonproteobacteria (rCAC), the amount of ATP to synthesize a gram of biomass from CO2 was calculated from genome sequences via metabolic maps. The eleven central carbon metabolites needed to synthesize biomass were all less expensive to synthesize via the rCAC (66%–89% of the ATP needed to synthesize them via CBB). Differences in cell compositions did result in differing demands for metabolites among the organisms, but the differences in cost to synthesize biomass were small among organisms that used a particular pathway (e.g. rCAC), compared to the difference between pathways (rCAC versus CBB). The rCAC autotrophs averaged 0.195 moles ATP per g biomass, while their CBB counterparts averaged 0.238. This is the first in silico estimate of the relative expense of both pathways to generate biomass. Their research is published in the Oxford journal FEMS Microbiology Letters. Their paper was selected as Editor’s Choice for the month of March, 2016!
The gammaproteobacterium Thiomicrospira crunogena XCL-2 is an aerobic sulfur-oxidizing hydrothermal vent chemolithoautotroph that has a CO2 concentrating mechanism (CCM), which generates intracellular dissolved inorganic carbon (DIC) concentrations much higher than extracellular, thereby providing substrate for carbon fixation at sufficient rate. This CCM presumably requires at least one active DIC transporter to generate the elevated intracellular concentrations of DIC measured in this organism. Authors Kristy Menning, (USF Dept. of Psychiatry), Balaraj Menon, (Univ. of Southern Mississippi, Hattiesburg, MS), Gordon Fox, (USF Integrative Biology), Kathleen (KT) Scott, (USF Integrative Biology) and the USF MCB4404L 2012 class conducted a study on the bacteria where the half-saturation constant (KCO2) for purified carboxysomal RubisCO was measured (276 ± 18 µM) which was much greater than the KCO2 of whole cells (1.03 µM), highlighting the degree to which the CCM facilitates CO2 fixation under low CO2 conditions. To clarify the bioenergetics powering active DIC uptake, cells were incubated in the presence of inhibitors targeting ATP synthesis (DCCD) or proton potential (CCCP). Incubations with each of these inhibitors resulted in diminished intracellular ATP, DIC, and fixed carbon, despite an absence of an inhibitory effect on proton potential in the DCCD-incubated cells. Electron transport complexes NADH dehydrogenase and the bc1 complex were found to be insensitive to DCCD, suggesting that ATP synthase was the primary target of DCCD. Given the correlation of DIC uptake to the intracellular ATP concentration, the ABC transporter genes were targeted by qRT-PCR, but were not upregulated under low-DIC conditions. As the T. crunogena genome does not include orthologs of any genes encoding known DIC uptake systems, these data suggest that a novel, yet to be identified, ATP- and proton potential-dependent DIC trans-porter is active in this bacterium. This transporter serves to facilitate growth by T. crunogena and other Thiomicrospiras in the many habitats where they are found. Their study is published in the Archives of Microbiology.
Understanding the processes driving the distribution of mid-water prey such as euphausiids and lanternfish is important for effective management and conservation. In the vicinity of abrupt topographic features such as banks, seamounts and shelf-breaks, mid-water faunal biomass is often elevated, making these sites candidates for special protection. Authors Tom Letessier, (Univ. of Western Australia, Crawley, WA, AU), Martin Cox, (Australian Antarctic Division, Kingston, AU), Jessica Meeuwig, (Univ. of Western Australia, Crawley, WA, AU), Philipp Boersch-Supan, (USF Integrative Biology), and Andrew Brierley, (Univ. of St. Andrew, Fife, UK) investigated the spatial distribution of water column acoustic backscatter - a proxy for macrozoo-plankton and fish biomass - in the 9 km transition zone between the pelagos and coral atolls in the Chagos Archipelago (6° N, 72° E). The purpose was to determine the magnitude and distance over which bathymetry may enhance biomass in the mid-water, and thereby identify the scale over which static topographic features could influence the open ocean. Two distinct sound scattering layers were identified, from the surface to 180 m and from 300 to 600 m, during daytime. Both layers exhibited significant increases in backscatter near features. Close to features, the shallow layer backscatter was ca. 100 times higher and was driven partly by increasing numbers of larger individuals, evident as single target echoes. The authors determined the regional scale of influence of features on pelagic biomass enhancement to be ca. 1.8 km in the Chagos Archipelago, and suggest possible ecological explanations that may support it. The authors report that their approach determining the scale of influence of bathymetry should be applied during the process of marine reserve design, in order to improve protection of mid-water fauna associated with topographical features, such as seamounts and coral reefs. Their study is published in the journal Marine Ecology Progress Series.
Effective population size is a fundamental parameter in population genetics, and factors that alter effective population size will shape the genetic characteristics of populations. Habitat disturbance may have a large effect on genetic characteristics of populations by influencing immigration and gene flow, particularly in fragmented habitats. Authors Aaron Schrey, (Armstrong State Univ., Savannah, GA), Alexandria Ragsdale, (Armstrong State Univ., Savannah, GA), Earl McCoy, (USF Integrative Biology) and Henry Mushinsky, (USF Integrative Biology) used the Florida Sand Skink (Plestiodon reynoldsi) to investigate the effect of fire-based habitat disturbances on the effective population size in the highly threatened, severely fragmented, and fire dependent Florida scrub habitat. They screened seven microsatellite loci in 604 individuals collected from 12 locations at Archbold Biological Station. Archbold Biological Station has an active fire management plan and detailed records of fires dating to 1967. Their objective was to determine how the timing, number, and intervals between fires affect effective population size, focusing on multiple fires in the same location. Effective population size was higher in areas that had not been burned for more than ten years and decreased with number of fires and shorter time between fires. A similar pattern was observed in abundance: increasing abundance with time-since-fire and decreasing abundance with number of fires. The ratio of effective population size to census size was higher at sites with more recent fires and tended to decrease with time-since-last-fire. The results of their study suggest that habitat disturbances, such as fire, may have a large effect in the genetic characteristics of local populations and that Florida Sand Skinks are well adapted to the natural fire dynamics required to maintain Florida scrub. Their paper is published in the Journal of Heredity .
Multi-drug resistant fecal bacteria (MRF) including gram-negative Escherichia coli and positive Enterococcus faecium are of prime concern to food safety and public health. This study was performed to test efficacy of a natural antimicrobial, polymeric chitosan-based nanoparticles combined with ZnO to in situ intervention. Authors Alya Limayem, (USF Dept. of Cell Biology, Microbiology and Molecular Biology), Andrew Micciche, (USF Dept. of Cell Biology, Microbiology and Molecular Biology), Edward Haller, (USF Integrative Biology), Chao Zhang, (USF Dept. of Cell Biology, Microbiology and Molecular Biology), and Shyam Mohapatra, (USF College of Medicine, Dept. of Internal Medicine) examined the effects of nanoparticles (NPs) of chitosan, ZnO alone and a combination of chitosan and ZnO, (CZNPs) at 1:1 on co-cultured nosocomial MRFs and a wild type (WT) through the minimal inhibitory concentration (MIC) test which conforms to National Standards, NCCLS. Toward elucidating visually the mechanistic effects of NPs alone and CZNPs on MRF and WT strains, Transmission Electronic Microscopy (TEM) was performed. While chitosan 1 (C1) and 2 (C2) alone with a molecular weight of 3 kDa and 50 kDa, respectively inhibited resistant E. coli strain (E. coli BAA-2471), they were ineffective at a concentration less than 5 mg/mL on either E. faecium strains and the co-cultures. ZnO and chitosan alone did not exhibit optimal effects on MRF strains and cultures alone. However, the MRF co-culture, E. coli BAA-2471 and E. faecium 1449 was completely inhibited by the C1ZNPs with an average minimal MIC of 0.781 mg/mL, and a maximal MIC of 1.302 mg/mL. Synergism of C1ZNPs over C2ZNPs proved to be predominantly inhibitive of MRF over WT co-cultures. Further TEM analyses demonstrated attachment and lysis of MRFs at 16h past treatment. Conclusively, CZNPs inhibit MRF co-cultures and is a promising in vivo intervention agent. Their study is published in the Kenkyu Journal of Nanotechnology and Nanoscience.
The impact of widespread and common environmental factors, such as chemical contaminants, on infectious disease risk in amphibians is particularly important because both chemical contaminants and infectious disease have been implicated in worldwide amphibian declines. Authors Uthpala Jayawardena, (Univ. of Peradeniya, Peradeniya, LK), Jason Rohr, (USF Integrative Biology), Ayanthi Navaratne, (Univ. of Peradeniya, Peradeniya, LK), Priyanie Amerasinghe, (International Water Management Institute, Hyderabad, Andhra Pradesh, IN), and Rupika Rajakaruna, (Univ. of Peradeniya, Peradeniya, LK) report on the lone and combined effects of exposure to parasitic cercariae (larval stage) of the digenetic trematode, Acanthostomum burminis, and four commonly used pesticides (insecticides: chlorpyrifos, dimethoate; herbicides: glyphosate, propanil) at ecologically relevant concentrations on the survival, growth, and development of the common hourglass tree frog, Polypedates cruciger Blyth 1852. There was no evidence of any pesticide-induced mortality on cercariae because all the cercariae successfully penetrated each tadpole host regardless of pesticide treatment. In isolation, both cercarial and pesticide exposure significantly decreased frog survival, development, and growth, and increased developmental malformations, such as scoliosis, kyphosis, and also edema and skin ulcers. The authors found that the combination of cercariae and pesticides generally posed greater risk to frogs than either factor alone by decreasing survival or growth or increasing time to metamorphosis or malformations. The exception was that lone exposure to chlorpyrifos had higher mortality without than with cercariae. They report that, consistent with mathematical models that suggest that stress should increase the impact of generalist parasites, the weight of the evidence from the field and laboratory suggests that ecologically relevant concentrations of agrochemicals generally increase the threat that trematodes pose to amphibians, highlighting the importance of elucidating interactions between anthropogenic activities and infectious disease in taxa of conservation concern. Their study is published in the journal EcoHealth.
Recently, Chantale Bégin, Instructor in USF Integrative Biology, taught a course titled Tropical Marine Ecosystems (BSC 4933). It was 3-credit course that was held half on the USF campus and half in the British Virgin Islands. While at USF, 20 students learned about mangroves, seagrasses and coral reef ecosystems, learning to identify common Caribbean invertebrates (including corals), fish and macrophytes, and acquired scientific diver in training status with AAUS (the American Academy for Underwater Science). After this initial training at USF, students traveled to Tortola, where they boarded the 112ft sailing vessel Argo. Over the 10 days that the class was aboard Argo, they sailed to several sites on the islands Tortola, Peter Island, Virgin Gorda, Guana, Sandy Spit and Jost Van Dyke. They gained experience using scuba diving and snorkeling to carry out standard benthic surveys and gather data on coral reefs, seagrass beds and mangroves. Students each completed 12 dives while in the BVI, and thereby gained full AAUS scientific diver status. After the BVI, the class met again in Tampa for a couple of days to analyze the data they collected. Among other things, they compared coral reef communities at various depth, quantified invertebrate density and richness in seagrass beds and mangrove roots, and examined the use of mangroves by several species of reef fishes.
Terry-René Brown, (Ph.D. Candidate, Scott lab, USF Integrative Biology), has been awarded a 2016-17 Fulbright-Schuman European Union Affairs Program grant for collaborative research on two environmental policy projects in the European Union (EU). The title of her proposal was “Climate Change and Biodiversity: Science and Policy in the European Union.” The Fulbright grant will provide René the opportunity to work with Dr. Valerie Kapos, Head of the Programme for Climate Change and Biodiversity at the United Nations Environment Programme-World Conservation Monitoring Centre (UNEP-WCMC), on a project investigating the impacts of climate change mitigation on biodiversity. The project will involve identifying the climate change mitigation measures the EU financially supports and assessing the positive and negative impacts these measures may have on biodiversity. Results from these studies will help direct UNEP-WCMC program priorities and will also be used to inform the EU and member states of the effects of climate change mitigation policies on biodiversity with the objective of promoting measures that enhance biodiversity and recommending safeguards for those that diminish biodiversity. René’s second host will be the Netherlands Institute of Ecology (NIOO-KNAW) with Dr. Lisette de Senerpont Domis, Head of the Aquatic Knowledge Centre Wageningen. This project will involve a large-scale meta-analysis of climate, biodiversity and water quality data collected in the Netherlands as a requirement of EU law under the Water Framework and Bathing Water Directives. The proposed project would involve analyzing these data along with historical and meteorological data to determine the relationships between climate, biodiversity, and water quality, and to determine the extent to which monitoring targets have been met. During her stay in the Netherlands, René and her host will convene a water management workshop, inviting water managers from other EU member states (e.g., Belgium, Czech Republic, Greece, Italy, Poland, and Spain); the goals of the workshop are to present and discuss their results and to invite related presentations from other water managers, to help shape water quality monitoring practices in the EU. René hopes that the results of both studies will advance the state of climate change policy and biodiversity protection in the EU, and will be applicable to the US and beyond. Congratulations on receiving such a prestigious grant!
Sarah Burgan, Master’s degree candidate in the Martin lab (USF Integrative Biology), was recently awarded an Animal Behavior Society student research grant for her studies on house sparrows. Sarah’s proposal was titled "Repeated Parasite Exposure: Implications for Host Defense Strategy and Transmission." The aim of her research is to investigate the defense strategies (i.e., resistance and tolerance) of house sparrows upon exposure to West Nile virus. By connecting physiological processes within hosts to their competence to transmit parasites, she believes that researchers may better understand the influence of individual hosts on population- and community-level disease dynamics. A reviewer of Sarah’s application wrote: “The ABS student grant proposal entitled “Repeated parasite exposure: implications for host defense strategy and transmission” has significant broad implications in two areas: 1) it concerns the impact of the interaction of disease tolerance and resistance at different levels of biological structure --the individual host and the population as a virus reservoir; and 2) it concerns a significant disease threat to less tolerant bird species as well as a humans. These two points were succinctly reviewed as well as the background of the relevant organisms and virus making this integrative biology study proposal interesting to read. The experimental procedure is clearly indicated including how the threshold and resistance will be measured by specific parameters concerning physiology. The predictions and rationale for the predictions are clearly stated for the measured parameters. It was good to see the thought that was put into the statistical analysis beforehand.” Congratulations, Sarah!
Sewage spills can release antibiotic resistant bacteria to surface waters, contributing to environmental reservoirs and potentially impacting human health. Vancomycin resistant enterococci (VRE) are nosocomial pathogens that have been detected in environmental habitats including soil, water, beach sands and wildlife feces. However, VRE harboring vanA genes that confer high-level resistance have infrequently been found outside of clinical settings in the U.S. Suzanne Young, (USF Integrative Biology), Bina Nayak, (Water Research Manager, Pinellas County Utilities, Pinellas county, FL), Shan Sun, (Dept. of Crop and Soil Environmental Sciences, Virginia Tech, Blackburg, VA), Brian Badgley, (Dept. of Crop and Soil Environmental Sciences, Virginia Tech, Blackburg, VA), Jason Rohr, (USF Integrative Biology) and Valerie (Jody) Harwood, (USF Integrative Biology) conducted a study of culturable Enterococcus faecium harboring the vanA gene in water and sediment up to three days after a sewage spill, and the qPCR signal for vanA persisted for an additional week. Culturable enterococci levels in water exceeded recreational water guidelines for two weeks following the spill, declining about five orders of magnitude in sediments and two orders of magnitude in the water column over six weeks. Analysis of bacterial taxa via 16S rRNA gene sequencing showed changes in community structure through time following the sewage spill in both sediment and water. The spread of opportunistic pathogens harboring high level vancomycin resistance genes beyond hospitals and into the broader community and associated habitats is a potential threat to public health, requiring further studies examining the persistence, occurrence and survival of VRE in different environmental matrices.
Journal of Applied and Environmental Microbiology. Their research is featured in an article in Florida Today online news. Suzanne is interviewed on WMNF 88.5FM Radio, whose website carries an article about the study. The study is also featured on WMNF News Channel 10 TV and carried in the Tampa Bay Times newspaper.
Humans are altering the distribution of species by changing the climate and disrupting biotic interactions and dispersal. A fundamental hypothesis in spatial ecology suggests that these effects are scale dependent; biotic interactions should shape distributions at local scales, whereas climate should dominate at regional scales. If so, common single-scale analyses might misestimate the impacts of anthropogenic modifications on biodiversity and the environment. However, large-scale datasets necessary to test these hypotheses have not been available until recently. Authors Jeremy Cohen, (USF Integrative Biology), David Civitello, (USF Integrative Biology), Amber Brace, (USF Integrative Biology), Erin Feichtinger, (USF Integrative Biology), C. Nicole Ortega, (USF Integrative Biology), Jason Richardson, (USF Integrative Biology), Erin Sauer, (USF Integrative Biology), Xuan Liub, (Chinese Acad. of Sciences, Beijing, CN) and Jason Rohr (USF Integrative Biology) conducted a cross-continental, cross-scale (almost five orders of magnitude) analysis of the influence of biotic and abiotic processes and human population density on the distribution of three emerging pathogens: the amphibian chytrid fungus implicated in worldwide amphibian declines and West Nile virus and the bacterium that causes Lyme disease (Borrelia burgdorferi), which are responsible for ongoing human health crises. In all three systems, the authors show that biotic factors were significant predictors of pathogen distributions in multiple regression models only at local scales (~102-103km2), whereas climate and human population density always were significant only at relatively larger, regional scales (usually >104km2). Spatial autocorrelation analyses revealed that biotic factors were more variable at smaller scales, whereas climatic factors were more variable at larger scales, as is consistent with the prediction that factors should be important at the scales at which they vary the most. Finally, no single scale could detect the importance of all three categories of processes. These results highlight that common single-scale analyses can misrepresent the true impact of anthropogenic modifications on biodiversity and the environment. Their study is published in the journal PNAS.
In January Stephanie Gervasi, Sarah Burgan, Nathan Burkett-Cadena, Aaron Schrey, Hassan Hassan, Tom Unnasch and Lynn (Marty) Martin presented a talk titled “Vector preferences and host defenses in the West Nile virus system: A role for avian stress hormones?” at the annual meeting of the Society for Integrative and Comparative Biology in Portland, Oregon. Their research showed that significantly more blood was taken by mosquitos from birds that exhibited stress than birds not expressing stress hormones in their blood. Their studies went on to show that mosquitos fed on blood from birds under stress lay more eggs, and lay them more quickly after feeding, implying that mosquitos feeding on stressed populations of animals produce larger populations of mosquitos more rapidly, spreading disease more rapidly. Read more about their research here.
CONGRATULATIONS TO OUR FALL 2015 GRADUATES!
Christy Foust - Ph.D. (Richards/Harwood labs)
Nate Goddard - Ph.D. (Crisman lab)
Samantha Wilber - M.S. (McCoy/Mushinsky lab)
We wish you all the best in the future, and great success along the way!