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Disease is one of the evolutionary forces shaping populations. Recent studies have shown that epidemics like avian pox, malaria, or mycoplasmosis have affected passerine population dynamics, being responsible for the decline of some populations or disproportionately killing males and larger individuals and thus selecting for specific morphotypes. However, few studies have estimated the effects of an epidemic by following individual birds using the capture-recapture approach. Because avian pox can be diagnosed by direct examination of the birds, we are here able to analyze, using multistate models, the development and consequences of an avian pox epidemic affecting in 1996, a population of Serins (Serinus serinus) in northeastern Spain. The epidemics lasted from June to the end of November of 1996, with a maximum apparent prevalence rate > 30% in October. However, recapture rate of sick birds was very high (0.81, range 0.37-0.93) compared to that of healthy birds (0.21, range 0.02-0.32), which highly inflated apparent prevalence rate. This was additionally supported by the low predicted transition from the state of being uninfected to the state of being infected (0.03, SE 0.03). Once infected, Serin avian pox was very virulent with (15-day) survival rate of infected birds being of only 0.46 (SE 0.17) compared to that of healthy ones (0.87, SE 0.03). Probability of recovery from disease, provided that the bird survived the first two weeks, however, was very high (0.65, SE 0.25). The use of these estimates together with a simple model, allowed us to predict an asymptotic increase to prevalence of about 4% by the end of the outbreak period, followed by a sharp decline, with the only remaining infestations being infected birds that had not yet recovered. This is in contrast to the apparent prevalence of pox and stresses the need to estimate recapture rates when estimating population dynamics parameters.

When endeavoring to make informed decisions, conservation biologists must frequently contend with disparate sources of data and competing hypotheses about the likely impacts of proposed decisions on the resource status. Frequently, statistical analyses, modeling (e.g., for population projection) and optimization or simulation are conducted as separate exercises. For example, a population model might be constructed, whose parameters are then estimated from data (e.g., ringing studies, population surveys). This model might then be used to predict future population states, from current population estimates, under a particular management regime. Finally, the parameterized model might also be used to evaluate alternative candidate management decisions, via simulation, optimization, or both. This approach, while effective, does not take full advantage of the integration of data and model components for prediction and updating; we propose a hierarchical Bayesian context for this integration. In the case of American black ducks (Anas rubripes), managers are simultaneously faced with trying to extract a sustainable harvest from the species, while maintaining individual stocks above acceptable thresholds. The problem is complicated by spatial heterogeneity in the growth rates and carrying capacity of black ducks stocks, movement between stocks, regional differences in the intensity of harvest pressure, and heterogeneity in the degree of competition from a close congener, mallards (Anas platyrynchos) among stocks. We have constructed a population life cycle model that takes these components into account and simultaneously performs parameter estimation and population prediction in a Bayesian framework. Ringing data are used to develop posterior predictive distributions for harvest mortality rates, given as input decisions about harvest regulations. Population surveys of black ducks and mallards are used to obtain stock-specific estimates of population size for both species, for inputs into the population life-cycle model. These estimates are combined with the posterior distributions for harvest mortality, to obtain posterior predictive distributions of future population status for candidate sets of regional harvest regulations, under alternative biological hypotheses for black duck population dynamics. These distributions might then be used for both the exploration of optimal harvest policies and for sequential updating of model posteriors, via comparison of predictive distributions to future survey estimates of stock-specific abundance. Our approach illustrates advantages of MCMC for integrating disparate data sources into a common predictive framework, for use in conservation decision making.

Research in wildlife conservation and management often affects decisions made by managers. Improving understanding through applied research is key to advancing the ability to manage birds and other organism sefficiently. Indeed, many papers from EURING 2003 and previous EURING meetings describe research on problems of pressing management concern. In this session, we focus on a subset of studies in which modeling and statistical estimation is explicitly connected to management decision-making. In these decision–centric studies, data are gathered and models are constructed with the explicit intention of using the resulting information to inform decisions about conservation. Whereas ecological models often produce information of value to decision makers, decision models explicitly include two additional features. First, management options are modeled via decision variables that link to system attributes that are directly responsive to management actions, such as harvest and habitat management. Second, certain outcomes are assigned value, via an objective or utility function. Both of these features involve factors beyond the usual consideration of ecological modeling; the first implies the presence of one or more “decision makers”, and the second characterizes the societal preferences of each possible outcome resulting from a prospective decision. Our plenary paper, by Tim Haas (Haas, 2004), ventures the furthest into the realm of human behavior and societal processes by modeling the political context for conservation of the endangered cheetah (Acinonyx jubatus) in Africa. Haas shows that scientific information (e.g., population monitoring and population viability analyses) reaches decision makers through multiple pathways, each of which can modify or reinterpret the information signal. A predictive understanding of the country’s political as well as ecological processes is essential. Hass uses a system of interacting ecological and political influence diagrams to capture the stochastic, temporal processes of managing cheetah population in Kenya. The model predicts likely anagement decisions made by various actors within these countries, (e.g., the President, the Environmental Protection Agency, and rural residents) and the resulting probability of cheetah extinction following these decisions. By approaching the problem in both its political and ecological contexts one avoids consideration of decisions that, while beneficial from a purely conservation point of view, are unlikely to be implemented because of conflicting political objectives. Haas’s analysis demonstrates both the promise and challenges of this type of modeling, and he offers suggestions for overcoming inherent technical difficulties such as model calibration. The second paper, by Simon Hoyle and Mark Maunder (Hoyle & Maunder, 2004), uses a Bayesian approach to model population dynamics and the effects of commercial fishing bycatch for the eastern Pacific Ocean spotted dolphin (Stenella attenuata). Their paper provides a good example of why Bayesian analysis is particularly suited to many management problems. Namely, because it allows the integration of disparate pieces of monitoring data in the simultaneous estimation of population parameters; allows forincorporation of expert judgment and data from other systems and species; and provides for explicit consideration of uncertainty in decision–making. Alternative management scenarios can then be explored via forward simulations. In the third paper, Chris Fonnesbeck and Mike Conroy (Fonnesbeck & Conroy, 2004) present an integrated approach for estimating parameters and predicting abundance of American black duck (Anas rubripes) populations. They also employ a ayesian approach and overcome some of the computational challenges by using Markov chain–Monte Carlo methods. Ring–recovery and harvest data are used to estimate fall age ratios under alternative reproductive models. These in turn are used to predict abundance of black ducks in each of 3 breeding areas. Finally, calibration of model parameters is obtained by comparing predicted with observed abundance. Although not currently implemented, the authors discuss how a Bayesian approach can be integrated into decision–making procedures using conditional modeling and application of reinforcement or machine learning. The next paper, by Martin Drechler and Franz Wätzold (Drechler & Wätzold, 2004), considers the problem of optimally allocating a conservation budget over time to maximize the survival probability of an endangered species. This must be done in the presence of uncertainty both about the biological system (e.g., probability of extinction under alternative plans), as well as about the availability of future funding. On the one hand, it would be undesirable to imprudently spend money now that might be needed for future conservation effort, when funds may be limited. On the other hand, failure to take action (and thus spend funds) sooner might lead to a higher probability of extinction. Provided estimates of uncertainty in funding, a model for trend in funding, and a model relating funding levels to viability, stochastic dynamic programming can be used to solve for an optimal amount of expenditure during any budget period. The final paper, by Clint Moore and Bill Kendall (Moore & Kendall, 2004), examines the costs incurred when uncalibrated indices to abundance are used in lieu of unbiased abundance estimates to make management decisions. Indices are often used instead of abundance estimates in the belief that the latter are too difficult and expensive. Moore and Kendall analyzed the impacts of using indices when making silvicultural decisions for the joint benefit of two bird populations, an endangered woodpecker and a shrub–nesting neotropical migrant. They computed the expected cost of uncertainty in the relationship between the onitoring index and population size, in currency units of the composite objective for both species. The authors found that substantial degradation of decision value can occur, depending on how uncertain the relationship between the index and true abundance. The results have important implications for managers, who may endeavor to cut costs by using index–based methods, while in the process incur these hidden costs of loss of decision utility. The five papers summarized above provide a good sampling of applications and methodological approaches, but are not a comprehensive coverage of the topic. For useful introductions to decision theory and methods, we suggest that readers consult Lindley (1985) or Clemen & Reilly (2001). A more detailed coverage of optimal decision–making, decision–making under uncertainty, and adaptive resource management is provided in Williams et al. (2002: chapters 21–25).

Few fields in modern ecology have developed as fast as the analysis of marked individuals in the study of wild animal populations (Seber & Schwarz, 2002). This is the topic of EURING Conferences, which from 1986 have been the premier forum for advances in capture-recapture methodology. In this sense, EURING Conferences still maintain the flavour that originally inspired scientific meetings: to disseminate the very last findings, ideas and results on the field. Traditionally, EURING Conferences have been published in the form of Proceedings, which because of their relevant content, become a required reading to anyone interested in the capture-recapture methodology. EURING 2003 was held in Radolfzell (Germany), hosted by the Max Planck Research Centre for Ornithology, and the Proceedings appear as a special issue of Animal Biodiversity and Conservation. The full title of the 2003 meeting was “The quantitative study of marked individuals in ecology, evolution and conservation biology”, which stands for one of the main aims of the meeting: to establish the capture-recapture approach as one of the standard methodologies in studies within these fields. One of the shared views is that capture-recapture methodologies have reached a considerable maturity, but the need still exists to spread their use as a “standard” methodology. The nice review paper by Lebreton et al. (1993) in Trends in Ecology and Evolution is still applicable, in that general ecologists and evolutionary biologists still resist their general use. The same applies to conservation biology, where the analysis of marked individuals may also be a key tool in its development. We hope, with the spread of 2003 Proceedings, to help to fill this gap. The Proceedings follow the same general structure as the Conference. We organised the EURING meeting in 10 technical sessions, covering what we considered as fastest growing areas in the field. We appointed for each session, two chairs, which were charged with selecting 4-7 talks on the topic of their session. Each session additionally included a plenary conference intended to summarise or to provide a general but synthetic flavour of the topic. As a novelty in EURING conferences, we asked session chairs to include at least one talk dealing with study species other than birds. This is the result of a heated but fruitful discussion at EURING 2000 in Point Reyes, and fits with the general aim to spread the capture-recapture methodology beyond zoological groups: although EURING as an organization, deals with birds, and conferences have traditionally focused on this group, the capture-recapture approach is becoming a standard way to address biologically relevant questions on populations and individuals (Schwarz, 2002), for any zoological group. This volume, contains several nice examples of taxa other than birds. As far as possible, we selected chairs so that each session was delineated with a good balance between the biological and the statistician emphasis. This balance has in fact characterised EURING conferences, which in addition to the workshop atmosphere always present, has lead to very fruitful exchanges. Session The quantitative study of marked individuals in ecology, evolution and conservation biology: a foreword to the EURING 2003 Conference which in addition to the workshop atmosphere always present, has lead to very fruitful exchanges. Session chairs were also asked to act as editors for the papers within their session. All the papers were hence subjected to peer review, as in any other issue of Animal Biodiversity and Conservation, and presentation of the paper in the Conference did not assure publication in the Proceedings. This has lead to an even higher quality of the papers presented at the Conference. Editors were additionally asked to write a short summary on their session. Given that these summaries also present the views of the Editors on the different topics presented, we have preferred each introduction to appear as a short paper in the front of each one of the sessions, so that it can be cited as a regular paper. The Proceedings start with the Honour Speaker Talk by James Nichols (Nichols, 2004). This talk is traditionally the last one in the Conference, but we think that it nicely summarises how and why capture-recapture has developed to its current healthy state. The talk is in fact a tribute to David Anderson, to whom, as Nichols says, all of us are more or less in debt. Hence, we have preferred to move the Honour Talk to the front position of the Proceedings, and we would like this to be our humble tribute to David. At the end of the Proceedings appear a few papers which were presented in poster format, and a paper summarising several of the main topics presented at the traditional short course on capture-recapture, this time organized by the unflagging Evan Cooch. We would like to thank all the people who helped in one way or another to the successful completion of the EURING Conference and the Proceedings. We thank to the Session Chairs, their dedication and enthusiasm in organizing the sessions and also in editing the different papers. All their names appear in the front page of the Proceedings as credits. We thank Wolfgang Fiedler for the local organization of the event: a very difficult and exhausting task that is not always properly recognized. Jean Clobert, although unfortunately unable to attend the Conference, supported us with ideas and friendship meanwhile preparing the scientific program. Evan Cooch maintained the always successful web page (which probably will also become a classic in EURING conferences…), and organized the traditional course on capture-recapture. Charles Francis very efficiently organized the poster session and acted as editor for the papers sent for publication. Finally we thank the Ministerio de Ciencia y Tecnología for financial support to the publication of this special issue of Animal Biodiversity and Conservation (B.O.S. 2002-12283-E) and to the Natural History Museum of Barcelona for their support.

Infection with hepatitis B virus (HBV) can result in spontaneous resolution or chronic infection, which can remain asymptomatic or can progress to cirrhosis and/or hepatocellular carcinoma. The host immune response is thought to be a major determinant of the outcome of HBV infection and virus-specific cytotoxic T lymphocytes (CTL) can mediate immunity against the virus and cause liver pathology. Antigen-nonspecific innate lymphocytes may also contribute to HBV infection and liver disease, therefore, we examined the frequencies, phenotypes, cytolytic activities and cytokine profiles of circulating natural killer (NK) cells, CD1d-restricted invariant natural killer T ( iNKT) cells and CD56+ T cells in 102 asymptomatic HBV-infected patients and compared them with those in 66 uninfected control subjects. NK cells expressing low levels of CD56 (CD56dim) and CD56+ T cells were significantly expanded in the circulation of HBV-infected patients compared with control subjects. CD1d expression and iNKT cell frequencies were similar in both groups. Despite these expansions, we did not detect augmented natural or cytokine-induced cytotoxicity in the HBV-infected subjects. All lymphocyte populations studied produced interferon- γ (IFN- γ) significantly more frequently when taken from HBV-infected patients compared with when taken from healthy controls. Additionally, NK cells from the patients more frequently produced interleukin-10. As our HBV-infected cohort consisted of asymptomatic patients with low viral loads, we propose that CD56dim NK cells and CD56+ T cells control HBV infection by noncytolytic mechanisms. [ABSTRACT FROM AUTHOR]

The Escherichia coli ammonium transport protein (AmtB) has become the model system of choice for analysis of the process of ammonium uptake by the ubiquitous Amt family of inner membrane proteins. Over the past 6 years we have developed a range of genetic and biochemical tools in this system. These have allowed structure/function analysis to develop rapidly, offering insight initially into the membrane topology of the protein and most recently leading to the solution of high-resolution 3D structures. Genetic analysis has revealed a novel regulatory mechanism that is apparently conserved in prokaryotic Amt proteins and genetic approaches are also now being used to dissect structure/function relationships in Amt proteins. The now well-recognised homology between the Amt proteins, found in archaea, eubacteria, fungi and plants, and the Rhesus proteins, found characteristically in animals, also means that studies on E. coli AmtB can potentially shed light on structure/function relationships in the clinically important Rh proteins.

Cystatins, an amyloid-forming structural superfamily, form highly stable, domain-swapped dimers at physiological protein concentrations. In chicken cystatin, the active monomer is a kinetic trap en route to dimerization, and any changes in solution conditions or mutations that destabilize the folded state shorten the lifetime of the monomeric form. In such circumstances, amyloidogenesis will start from conditions where a domain-swapped dimer is the most prevalent species. Domain swapping occurs by a rearrangement of loop I, generating the new intermonomer interface between strands 2 and 3. The transition state for dimerization has a high level of hydrophobic group exposure, indicating that gross conformational perturbation is required for domain swapping to occur. Dimerization also occurs when chicken cystatin is in its reduced, molten-globule state, implying that the organization of secondary structure in this state mirrors that in the folded state and that domain swapping is not limited to the folded states of proteins. Although the interface between cystatin-fold units is poorly defined for cystatin A, the dimers are the appropriate size to account for the electron-dense regions in amyloid protofilaments.

This controlled laboratory study examined the efficacy of near-infrared spectroscopy (NIRS) and 31P-nuclear magnetic resonance (NMR) spectroscopy in measuring regional tissue oxygenation in a isolated, perfused hind limb model of tissue dysoxia. Isolated hind limb perfusion was carried out in 20 mongrel dogs and oxygen delivery was varied by manipulating either hemoglobin concentration, oxygen saturation, or flow. Hind limbs from anesthetized mongrel dogs (n = 20) were separated and isolated perfusion performed. NIRS probes for recording relative O2 saturation of tissue hemoglobin (HbO2) and cytochrome a,a3 and NMR probes for measuring 31P-high energy phosphates were placed over the limb. Measurements of physiologic parameters, blood gases, lactate, NIRS values for HbO2 and cytochrome a,a3 redox state, and 31P-phosphate levels were recorded at set intervals throughout the experiment. Measures of tissue oxygen consumption (VO2) correlated with tissue oxygenation as measured by HbO2 and cytochrome a,a3 redox state (NIRS), as well as by 31P-high energy phosphate levels (NMR) throughout the experiment. Delivery-dependent tissue oxygenation was detected at a higher DO2 by NIRS than by VO2 or NMR. Tissue oxygenation as measured by NIRS and NMR shows excellent correlation with oxygen delivery in an isolated, perfused model of shock. NIRS may allow early detection of tissue dysoxia using rapid non-invasive techniques.

Here, the solution structure of the Rhodobacter sphaeroides core light-harvesting complex beta polypeptide solubilised in chloroform:methanol is presented. The structure, determined by homonuclear NMR spectroscopy and distance geometry, comprises two alpha helical regions (residue -34 to -15 and -11 to +6, using the numbering system in which the conserved histidine residue is numbered zero) joined by a more flexible four amino acid residue linker. The C-terminal helix forms the membrane spanning region in the intact LH1 complex, whilst the N-terminal helix must lie in the lipid head groups or in the cytoplasm, and form the basis of interaction with the alpha polypeptide. The structure of a mutant beta polypeptide W(+9)F was also determined. This mutant, which is deficient in a hydrogen bond donor to the bacteriochlorophyll, showed an identical structure to the wild-type, implying that observed differences in interaction with other LH1 polypeptides must arise from cofactor binding. Using these structures we propose a modification to existing models of the intact LH1 complex by replacing the continuous helix of the beta polypeptide with two helices, one of which lies at an acute angle to the membrane plane. We suggest that a key difference between LH1 and LH2 is that the beta subunit is more bent in LH1. This modification puts the N terminus of LH1beta close to the reaction centre H subunit, and provides a rationale for the different ring sizes of LH1 and LH2 complexes., (Copyright 2000 Academic Press.)

In this study, a bioreactor subject to Starling flow in closed shell batch harvest mode was compared to two forms of additional forced extracapillary (EC) space convection including EC circulation and EC cycling. Despite the presence of Starling flow as the dominant EC convection mechanism in the batch harvest system, the bioreactor start up was fairly good. However, the antibody productivity of the batch harvest system fell off rapidly after day 20 resulting in only 4.5 g of antibody produced. EC circulation with flow parallel to the fibers had a slightly better start up than the batch harvest. However, the antibody productivity also dropped after day 20 with EC circulation, resulting in only 7.5 g of antibody produced. EC cycling with flow both parallel and perpendicular to the fibers resulted in a start up similar to that of EC circulation. However, in contrast to the other two systems, antibody productivity in the EC cycling system was stable over the 60-day experiment resulting in the production of 23 g of antibody. These results demonstrate the importance of inducing the proper flow distribution in the EC space to allow consistent and stable production in hollow fiber bioreactors., (Copyright 1999 John Wiley & Sons, Inc.)

The first study by nmr of the integral membrane protein, the bacterial light-harvesting (LH) antenna protein LH1 beta, is reported. The photosynthetic apparatus of purple bacteria contains two different kinds of antenna complexes (LH1 and LH2), which consist of two small integral membrane proteins alpha and beta, each of approximately 6 kDa, and bacteriochlorophyll and carotenoid pigments. We have purified the antenna polypeptide LH1 beta from Rhodobacter sphaeroides, and have recorded CD spectra and a series of two-dimensional nmr spectra. A comparison of CD spectra of LH1 beta observed in organic solvents and detergent micelles shows that the helical character of the peptide does not change appreciably between the two milieus. A significantly high-field shifted methyl signal was observed both in organic solvents and in detergent micelles, implying that a similar three-dimensional structure is present in each case. However, the 1H-nmr signals observed in organic solvents had a narrower line width and better resolution, and it is shown that in this case organic solvents provide a better medium for nmr studies than detergent micelles. A sequential assignment has been carried out on the C-terminal transmembrane region, which is the region in which the pigment is bound. The region is shown to have a helical structure by the chemical shift values of the alpha-CH protons and the presence of nuclear Overhauser effects characteristic of helices. An analysis of the amide proton chemical shifts of the residues surrounding the histidine chlorophyll ligand suggests that the local structure is well ordered even in the absence of protein-lipid and protein-pigment interactions. Its structure was determined from 348 nmr-derived constraints by using distance geometry calculations. The polypeptide contains an alpha-helix extending from Leu19 (position of cytoplasmic surface) to Trp44 (position of periplasmic surface). The helix is bent, as expected from the amide proton chemical shifts, and it is similar to the polypeptide fold of the previously determined crystal structure of Rhodopseudomonas acidophila Ac10050 LH2 beta (S. M. Prince et al., Journal of Molecular Biology, 1997, Vol. 268, pp. 412-423). It is concluded that the polypeptide conformation of this region may facilitate assembly of the LH complex.

Serologic testing, radio-telemetry and post-mortem diagnostic evaluations were used to investigate survival and causes of mortality among 17 coyotes (Canis latrans) in south-central Georgia (USA). Prevalence of canine heartworm (Dirofilaria immitis) microfilariae was lower (P = 0.057) among fall-captured (22%) than among winter-captured (75%) coyotes. Prevalence of heartworm was higher among adults than juveniles in the fall, but no significant difference was detected between animals captured in winter. Antibodies were found against canine parvovirus (65%), canine parainfluenza virus (59%), infectious canine hepatitis virus (41%), and Toxoplasma gondii (18%). Antibodies were not found to Brucella canis, canine coronavirus, five serovars of Leptospira interrogans, or canine distemper virus. Seroprevalence of canine parvovirus was lower (P = 0.009) among fall-captured animals (33%) than winter-captured animals (100%). The Kaplan-Meier estimate of annual survival was 0.500 for all animals. Juvenile survival did not differ (P = 0.79) from adult survival, but male survival (S = 0.217) was lower (P = 0.11) than female survival (S = 0.804). Two of nine (22%) mortalities were human-caused, one was due to concurrent canine parvovirus and canine distemper virus infections, one animal died of trauma, two were considered natural mortalities of unknown cause, and no cause of death could be determined for the remaining three animals. Natural mortality may be significant for coyotes in south-central Georgia, although there was no apparent link between exposure to pathogens and the animals' subsequent fate in our small sample.