Charles R. Brown, Ph.D. - US grants

The simulation component of the MDScope modeling environment, NAMD [19], continues to undergo improvement in both features and speed*. The latest version, NAMD2 (a complete rewrite of much of the NAMD code), is nearing a public release. NAMD2 goes further than any previous release in achieving the NAMD design goals of modifiability, speed, and parallel performance. NAMD2 is more modifiable than the original version, as demonstrated by the features added in the last year. The program now supports periodic boundary conditions, using either cutoff electrostatics or full Ewald electrostatics. It allows larger simulation steps using a triple-time-stepping scheme, which can allow some simulations to run at double the speed of the original method. NAMD2 has a prototype TCL-based scripting interface that permits users to alter some parts of the simulation without having to look at the program code at all. It now also employs the DPME algorithm for full electrostatics, developed by our collaborators at Duke University. NAMD2 supports a large number of parallel machines, including clusters of workstations, the SGI Origin 200 and Origin 2000, the IBM SP3, the Convex Exemplar, and the Cray T3E. The new structure of the program exhibits improved sequential speed, and better parallel performance [22] on machines with dozens to hundreds of processors. Improved algorithms and parallel efficiency, and the availability of large numbers of processor have resulted in an order of magnitude increase in the speed of simulations.

Animal Behavior Program

Non-technical Abstract



Title: Hormones, immunocompetence, and coloniality

PI: Brown, Charles R.

Proposal #: 9974733

Dr. Brown will study how the social environment affects levels of an animal's steroid hormones, and how these hormones may affect its immune response, in a colonial bird, the cliff swallow. The objectives are to determine (1) if there is a relationship between group size and levels of the hormones testosterone and corticosterone; (2) how social interaction (stress) is related to hormone levels; (3) if there is a relationship between hormone levels and immune function; and (4) how parasites affect hormone levels and immune function. Blood samples will be taken for hormone analysis and immune response tests done in the field on free-living individuals. Behavioral interactions such as fighting will be observed. Simple immunological tests will be performed to measure the birds' immune responses. Hormone levels and immune responses of birds occupying nests in which blood- sucking ectoparasites have been removed will be compared to those of birds in naturally infested nests.

This study will be the first attempt to study how hormone levels influence the evolution of group living. The results should lead to new insight into the poorly understood problem of why sociality evolves and why social groups vary in size. This study will be the first to address how hormones affect immune ability under natural conditions. If there is a link, the results will have potentially far-reaching biomedical implications.

0075199
Brown
This proposal seeks support for years 20-24 of a long-term study of demography and social behavior of cliff swallows in southwestern Nebraska. The investigators will continue to monitor survival, dispersal, and colony choice for a population of marked birds that now numbers 110,286 individuals. These data will be applied to other ongoing investigations of swallow population biology that will incorporate study of the effect of group size, and will also be used to study the long-term demographic consequences of a rare climatic event that occurred in the study area in 1996. Severe weather of this timing and magnitude has occurred in southwestern Nebraska only twice inn the last 125 years, and it reduced the population of cliff swallows by over 50%.
By applying the same methods and colony sampling schemes developed and used since 1982, this study will provide direct comparisons among years during a period spanning over two decades. Data gathered will be applied to work on (1) morphological evolution - directional selection on body size and selection for low levels of bilateral asymmetry brought about by the rare climatic event; (2) the relationship between colony size, steroid hormone levels, and immunocompetence - how levels of testosterone and corticosterone at different times during the breeding season vary with colony size; (3) transmission dynamics of ectoparasites and their associated alphaviruses; and (4) variation in colony size.

DESCRIPTION (provided by the applicant): The transmission and spread of most bird-associated arboviruses is poorly understood, in part because of the difficulty in reliably locating both hosts and vectors for sampling. Arthropod-borne alphaviruses are responsible for a variety of zoonotic human illnesses throughout the world, known or suspected to cause encephalitis, polyarthritis, hemorrhagic fever, and a variety of less serious diseases. Yet, what causes epidemics to occur in some areas, and how a virus persists in the interim between epidemics, is not well known. This study investigates the population dynamics of a recombinant alphavirus, Buggy Creek virus BCRV), in a natural system, in which the virus is associated with a vertebrate host, the cliff swallow Petrochelidon pyrrhonota), and an invertebrate vector, the cimicid swallow bug (Oeciacus vicarius). The project will determine the mechanisms that allow annual occurrence of the alphavirus in the population reintroduction by migratory birds vs over wintering in sedentary bugs), the extent of inter-group transmission by both birds and bugs, and how annual infection rates and transmission vary with ecological characteristics of colony sites. The virus subtypes at different sites will be characterized by sequencing, and the extent of evolutionary divergence at different sites will be related to patterns of site use and other ecological characteristics. The potential role of mosquitoes as a bridging vector to humans will be assessed. The work will rely on field collections of bugs for virus isolation and blood collection from birds, and will take advantage of a long-term dataset consisting of over 148,000 marked birds, for which survival and movement within the study area can be estimated. The project is one of the few to be able to investigate alphavirus transmission, persistence, and evolutionary divergence in a natural system where the foci of virus infections (i.e., colony sites) can be reliably identified and ecological hypotheses tested.

DESCRIPTION (provided by applicant): Arthritis continues to be a major source of morbidity worldwide. In most models of arthritis, neutrophils have been demonstrated to play a key role in the development of pathogenesis. The mechanism by which neutrophils mediate their effect, however, remains unknown. Lyme disease is caused by infection with the tick borne spirochete Borrelia burgdorferi (Bb). One major complication of this disease is the development of an inflammatory arthritis in most, but not all, patients untreated with antibiotics near the time of infection. Recently, using a mouse model of Lyme disease, we demonstrated a requirement for neutrophil recruitment into the joint tissue for the development of pathology. Joint homogenates from arthritis-susceptible mouse strains contained high levels of the chemoattractant KC, whereas joint homogenates from arthritis-resistant mouse strains did not. This suggested that polymorphisms in the initial host response to Bb infection by resident cells within the joint tissue led to the differential recruitment of neutrophils into the joints of resistant and susceptible mouse strains. Blocking the recruitment of neutrophils into the joint tissue in CXCR2 -/- mice resulted in a decrease in arthritis severity in both resistant and susceptible mouse strains. This application focuses specifically on the KC-mediated recruitment and activation of neutrophils in the ankle joint during Bb infection. Specific Aim 1 will test the hypothesis that recruitment of neutrophils into the infected joint by KC is necessary and sufficient for development of Lyme arthritis. Treatment of Bfc-infected mice with polyclonal antibody to KC or rKC will test for the requirement or sufficiency of KC for arthritis development. In Specific Aim 2 we will identify the cellular source of KC in joint tissue and test the hypothesis that sentinel cells within the joints of arthritis-resistant and -susceptible mice respond differently to Bb stimulation. Primary synovial fibroblasts from resistant and susceptible mouse strains will be co-cultured with Bb and the production of KC measured. Neutrophil modulation of the inflammatory response will also determined by the co-culture of neutrophils with synovial fibroblasts and measuring the production of KC in response to Bb stimulation. This proposal will define the role of KC in mediating the development of Lyme arthritis, but also addresses the broader issue of diversity within the innate immune response. As such these studies; may have important implications not only for Lyme disease, but for other inflammatory diseases as well.

This proposal is to continue a 25-year long study of demography and social behavior of cliff swallows in southwestern Nebraska. We will monitor survival, dispersal, and colony choice for a sample of marked birds that now numbers 158,373 individuals. This information will be applied to ongoing investigations of swallow population biology that incorporate study of the effect of group size, and will also be used to study the long-term consequences of two rare climatic events that occurred in the study area in 1996 and 2004. Severe weather of the timing and magnitude of these events has occurred in southwestern Nebraska only twice in the last 130 years. Data gathered will be applied to work on (1) the ecology and evolution of a virus associated with cliff swallows and their ectoparasites, in which we are studying how often this encephalitis-related virus is transmitted between colonies within the study area by birds, how colony use in a given year is related to prevalence of virus, whether bird movement is related to patterns of evolutionary divergence of virus subtypes within the study area, and how the virus affects survival of marked cliff swallows within and between years and thus to what degree it represents a disadvantage of living in colonies; and (2) morphological evolution and natural selection on breeding time, in which we are studying evolutionary changes in body size and extent of bilateral asymmetry in wings and tail brought about by the rare climatic events, and whether the widespread nesting failures in the 2004 breeding season will exert selection on breeding time and lead to earlier egg-laying in the population in successive generations.

DESCRIPTION (provided by applicant): Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed to relieve the symptoms of rheumatoid and osteoarthritis patients. New versions of these drugs (coxibs) act by inhibiting the activity of the cyclooxygenase (COX)-2 enzyme. COX-2 is responsible for the production of prostaglandins during inflammatory responses;which are the primary mediators of pain and swelling. While the new drugs represent a significant improvement over traditional NSAIDs, especially in avoiding unwanted gastrointestinal side-effects, there are concerns about side-effects with the new drugs as well. COX-2 is part of a complex system of eicosanoids that regulate the development and resolution of inflammatory responses. These enzymes and their products interact through several biochemical pathways and influence each others production. COX-2 was originally thought to contribute only to the development of inflammation. Recent studies, however, have suggested that COX-2-derived products may also contribute either directly or indirectly to the resolution phase of the inflammatory response. Thus, use of the new COX-2-inhibiting drugs may alleviate the symptoms of inflammatory diseases, but actually prevent resolution and healing of the underlying inflammation. This proposal uses a mouse model of arthritis caused by the spirochete, Borrelia burgdorferi, the agent of Lyme disease. In some mouse strains infection with this organism causes the development of a severe arthritis that peaks 2 to 3 weeks after infection, and then spontaneously resolves. Treatment of mice with the COX-2-inhibiting drugs, followed by infection with B. burgdorferi, causes the development of severe arthritis but prevents arthritis resolution. Because the eicosanoid pathways interact, there are several possible explanations for why this might occur. In this proposal we have designed specific aims that will allow us to determine which other pathways are involved in this response. We will: Specific Aim 1, determine if COX-1 can compensate for the loss of COX-2, and determine if the loss of anti-inflammatory prostaglandins are responsible for arthritis non-resolution;Specific Aim 2, determine if the loss of COX-2 causes a shunt of arachidonic acid into the leukotriene pathway;and Specific Aim 3, determine if the loss of COX-2 activity alters lipoxin production by neutrophils. This information will further our understanding of how inflammation is regulated and allow the design of more effective anti-inflammatory treatments.

This award continues a 30-year study of social behavior of colonially nesting cliff swallows in southwestern Nebraska. Annual survival and colony choice will be studied for a sample of over 200,000 individually marked birds by re-catching birds at different nesting colonies. The data gathered will examine how size of a nesting colony affects annual survival of cliff swallows and whether individuals use the same size colony each year. The research will also determine why nesting success in most seasonally breeding birds declines with time during the summer. Experimental treatment of cliff swallow colonies with insecticide creates conditions that stimulate some birds to nest much later in the summer than typically seen and will provide the opportunity to compare first-year survival of birds raised both early and late in the season.

Many kinds of animals live in groups of different sizes, including humans, and this research addresses fundamental questions about what factors create and maintain diversity in group sizes; what is discovered for swallows may apply to other species that live in social groups. Undergraduate students will be heavily involved, many of whom are women, minorities, and other underrepresented groups in research. This work will be relevant for conservation, because understanding colony choice and annual variation in survival probabilities of species such as cliff swallows could help in establishing management guidelines for similar migratory species that are declining.

Many social organisms live in groups of variable size. Group size has many important consequences, such as affecting the spread and transmission of infectious diseases both within the group and to members of other groups. This project seeks to understand why groups of variable size persist over long-term time scales. As we better understand what promotes variability in group size, we can better predict the extent to which the costs or benefits of group living will change over time. One popular but untested hypothesis is that climatic differences between years cause variation in food supply or in populations of parasites and pathogens, and this in turn causes the payoffs of different group sizes to vary annually. This project builds on a long-term study of a social bird, the cliff swallow, which lives in colonies of widely different sizes, and seeks to investigate whether changing selection on the animals' survival and reproductive success can explain annual variation in group size. The research addresses one of the most fundamental questions in evolutionary ecology.

This project will test the prediction that success of individuals will increase with group size in some years, decrease with group size in others, and remain unchanged in yet other years. It will be determined to what degree the birds' annual nesting success varies from year to year in colonies of different sizes. This will be investigated by systematically collecting data at 20-25 colonies each year. The work will determine the causes of variation in reproductive success by measuring the extent of parasite infestation, time of breeding, bird condition, and other factors. This study will promote better understanding of how group size affects individuals' lifetime reproductive success across long-term time scales, assist in interpreting the extensive variation in group size that is characteristic of many organisms, and reveal the potential influence of recent climatic changes on social behavior. The research will involve women, Native Americans, and students from the Great Plains, promoting STEM training of underrepresented groups with respect to gender, ethnicity, and geographic region.

All living organisms must defend themselves from disease-causing parasites and pathogens to which they are exposed. The typical way that such defense occurs is by resisting the pathogen or parasite, often through an immune response. Resistance by the host is the basis for much of modern medicine, in which the immune response is enhanced or replaced by various therapies. However, another defense is the tolerance of the parasite or pathogen without mounting any resistance, which (under certain circumstances) can be beneficial to the host, in part because tolerance does not require the host to incur the physiological cost of mounting an immune response. Plants are well known to tolerate various pathogens, but the ability of animals to tolerate parasites has only recently been recognized. This project documents how a colonial bird, the cliff swallow, has rapidly evolved (over 30 years) the ability to tolerate large numbers of blood-feeding parasitic bugs. By comparing the effects of these parasites on the birds in the 1980s versus their effects today, insight into conditions that favor the development of tolerance as a parasite defense in a social animal will be gained. The results will have wide relevance to understanding ways that animals (including humans) can potentially minimize the negative effects of parasites and the diseases sometimes associated with those parasites.

Parasite tolerance has been established as a key host defense in plant-parasite systems, but few empirical studies have explored the role of tolerance in animal host-parasite relationships. This research seeks to study the ecology and evolution of tolerance defense strategies against parasites in colonially nesting cliff swallows (Petrochelidon pyrrhonota) and their principal parasite, the swallow bug (Hemiptera: Cimicidae: Oeciacus vicarius). The work builds on a long-term field study and the relatively recent adoption of new nesting sites by cliff swallows where they have come into greater contact with their nest parasites. During the 1980s, bugs exerted severe effects on cliff swallow reproductive success, but subsequent observation suggests that the birds may have evolved greater tolerance to parasitism in the intervening 30 years. This research seeks to establish whether cliff swallows now better tolerate parasites and how the birds? anti-parasite behavior may be changing as a result. The novelty of this work is that it is the first to examine temporal changes in tolerance within a natural population. This research will involve undergraduate students and a postdoctoral scientist, and participation by a community college faculty member will facilitate involvement of urban minority students. Because enhancing tolerance by the host may be more effective in fighting inflammatory and autoimmune diseases than prescribing antibiotics (a strategy that promotes resistance to parasites), this research will encourage non-scientists to think about tolerance as a treatment option.

Abstract Inflammation is a beneficial response to infection or tissue damage and mediates the removal of microbial pathogens and restoration of the tissue to homeostasis. Occasionally the inflammatory response does not resolve properly and becomes chronic. Chronic inflammation is considered the underlying cause of many diseases of the modern world, such as arthritis, asthma, and many others, and much effort has gone into trying to block the development of inflammation. However, these approaches also increase the risk of serious infection due to simultaneous inhibition of host defense against microbial pathogens. Recent work has demonstrated that resolution of inflammation is an active process. Thus, therapeutics may be developed capable of inducing resolution of chronic inflammatory disease. The clearance of apoptotic cells (AC) from the inflammatory site has been identified as a key component of the resolution process. The uptake of AC by inflammatory macrophages (efferocytosis) induces their down-regulation of pro-inflammatory cytokines and up- regulation of anti-inflammatory mediators, increases efferocytosis, inhibits further neutrophil recruitment, and promotes tissue healing and homeostasis. In addition, the clearance of AC also prevents their undergoing secondary necrosis, leaking cytosolic contents and prolonging inflammation. Thus, a more complete understanding how efferocytosis modulates macrophages from pro-inflammatory to pro-resolution is needed. Eicosanoids are powerful lipid mediators derived from the metabolism of arachidonic acid. They mediate many aspects of the inflammatory response and play important roles in resolution. Omega-3 fatty acid metabolism produces a class of lipids called specific pro-resolving mediators (SPM) capable of inducing resolution of inflammation. My lab is interested in defining the mechanisms used by eicosanoids and SPM to induce the resolution of inflammatory disease. We use a mouse model of Lyme arthritis caused by infection of C3H mice with the spirochete, B. burgdorferi. This proposal has two specific aims: Aim 1 will explore the mechanism of how AC engulfment by inflammatory macrophages alters their function. We will determine the roles of various eicosanoid metabolic pathways (COX, 5-LOX and 12/15-LOX) and SPM in these responses. Aim 2 will explore the enhanced effect of activated AC (previous exposure to bacteria) on arthritis resolution, and the roles of eicosanoids and SPM in this process. Successful completion of these aims will lay the groundwork for further studies to elucidate the regulatory mechanisms of how, during an infectious inflammatory response, the system switches from pro-inflammatory to pro-resolution and the impact infectious agents have on this decision. These studies will broaden our understanding of inflammatory disease and may impact our ability to lessen chronic inflammation while sparing host defense.

Many social animals live in groups of different sizes. Individuals often seem to survive or reproduce better in groups of particular sizes in a given year, and ecologists have thus been puzzled as to why groups with less successful sizes continue to exist. One possibility is that changes in ecological conditions such as food availability or the presence of parasites, and/or climatic conditions such as how wet a year is, lead to certain group sizes being most successful in some years or in some areas, but different ones being most successful in other circumstances. However, whether or not the advantages of different sized groups fluctuate in this way over the long term and across broad geographic areas is unknown. This can only be addressed with long-term research that measures the success of animals in different groups in different years and geographic regions. This research will address this by measuring the reproductive success of individuals of a social bird, the cliff swallow, which breeds in colonies ranging from 1 to 6000 nests. Cliff swallows are found throughout much of western North America and are one of the most highly social land birds in the world. The work is investigating whether the costs and benefits of particular colony sizes change regularly enough among years to explain the long-term persistence of variation in group size. This research involves undergraduate students and offers them intensive research experience and training in field ecology. Public outreach is conducted by giving annual lectures at the Swallows Day festival at Mission San Juan Capistrano in California, appearance on national media associated with that event, and maintenance of a web site about the research and cliff swallows generally.

This proposal builds on a long-term study of a social bird, the cliff swallow, that lives in colonies of widely different sizes, and is investigating whether fluctuating selection on reproductive success can explain variation in group size. The data gathered will be applied to study annual reproductive success in colonies of different sizes from year to year. This is done by systematically collecting data on fledging success at up to 40 cliff swallow colonies each year. The work also focuses on the proximate ecological drivers of variation in reproductive success by examining the extent of ectoparasitism, breeding phenology, and other nest- and colony-based variables, allowing identification of climatic and other factors that lead to annual variation in reproductive success in different groups. The information gathered in this project, along with existing data on annual survival of breeding adults and first-year birds, will enable estimation of relative lifetime reproductive success of birds occupying different sized colonies. This study will allow better understanding of how group size affects fitness over the long term, assist in interpreting the extensive variation in group size that is characteristic of most social animals, reveal the potential influence of climatic variability on animal social behavior, and provide a test of the importance of fluctuating selection in generating and maintaining behavioral variation.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.