NORTH AMERICAN GRASSLAND BIRDS: AN UNFOLDING CONSERVATION CRISIS?

Abstract: The widespread and ongoing declines of North American bird populations that have affinities for grassland and grass-shrub habitats (hereafter referred to as grassland birds) are on track to become a prominent wildlife conservation crisis of the 21st century. There is no single cause responsible for the declines of grassland birds. Rather, a cumulative set of factors such as afforestation in the eastern United States, fragmentation and replacement of prairie vegetation with a modern agricultural landscape, and large-scale deterioration of western U.S. rangelands are the major causes for these declines. The North American Bird Conservation Initiative (NABCI) is a set of comprehensive and coordinated strategic actions modeled on the Joint Venture initiatives that were used to successfully implement the North American Waterfowl Management Plan. The NABCI is emerging as a potential broad-scale solution for conserving populations of grassland birds. Coordinating grassland bird conservation efforts with initiatives to stabilize and increase upland game birds that have strong affinities for grassland habitats—such as quail and prairie grouse—presents additional opportunities to leverage funding and resources that will positively impact virtually all species of North American grassland birds.     

Quality procedures in non-gynaecological cytology laboratories in England and Wales

All non-gynaecological cytology laboratories in England and Wales (n = 212) were surveyed by telephone. The aim was to investigate what concepts of quality applied in this context and to establish what tools and techniques of quality improvement were used. The overall response was 146 (69%). The respondents mainly comprised NHS Trusts and University Departments. The study showed that there was a diverse approach to quality. All types of quality assurance and customer focus procedure questioned were undertaken but to a varied extent; three laboratories (2%) used a complete range and three (2%) used no procedure at all. Accreditation was associated with staffing adequacy and use of surveys, but not quality assurance (QA) or user focus. Laboratories with a high priority for quality performed more QA and reported a higher staffing adequacy. Critical incident analysis was dependent on workload. Computerization did not affect quality procedures and involvement in the Breast Screening Programme did not result in different quality measures. The time since last update was independent of all factors and external quality assurance (EQA) was not widely available. The study suggested that an integrated approach to quality had not been adopted in English and Welsh cytology laboratories and that there may be a need for a more strategic approach with greater availability of EQA, guidelines on quality tools, closer linkage of accreditation and quality procedures and the production of minimum and ideal standards. The ideal standard could be the complete range of procedures, and the minimum standard could comprise those processes in most frequent use, i.e. critical incident analysis, correlation methods, action on information, analysis of what is done with diagnostic information, a complaints procedure and customer surveys.     

Modelling animal populations in changing landscapes

Models of Mobile Animal Populations (MAP models) simulate long-term land use changes, population trends and patterns of biological diversity on landscapes of 10³-10⁵ ha. MAP models can incorporate information about past land-use patterns and management practices and can project future patterns based on management plans. We illustrate this approach with an example of how implementation of a U.S. Forest Service management plan at the Savannah River Site in South Carolina, U.S.A., might influence population trends of Bachman's Sparrow Aimophila aestivalis, a relatively rare and declining species in southeastern pine forests. In this case, a management plan, largely designed to improve conditions for an endangered species, Red-cockaded Woodpecker Picoides borealis, may have a negative impact, at least in the short term, on another species of management concern, Bachman's Sparrow.
In a parallel processing version of the MAP models, a single landscape that would ordinarily be too large or detailed to be simulated on a single computer is subdivided into a number of smaller landscapes, and each landscape is simulated in parallel, either on a single multi-tasking machine or on a group of networked machines. With this approach we are attempting to determine just how large a landscape must be before the dynamics of a population within it are more or less independent of factors beyond the landscape boundaries.     

Ecological responses to nutrients in streams and rivers of the Colorado mountains and foothills

1. Abundance and composition of periphyton and benthic macroinvertebrates were treated as potential nutrient response variables for 74 streams in montane Colorado. The streams ranged from unenriched to mildly enriched with nutrients (N, P). 2. The study showed no meaningful relationship between periphyton biomass accumulation and concentrations of total or dissolved forms of nitrogen or phosphorus. Nutrient concentrations were also unrelated to periphyton and macroinvertebrate richness, diversity and community composition. Macroinvertebrate communities did, however, show a strong positive relationship to periphyton abundance. 3. A positive response of periphyton biomass to increasing nutrient concentrations has been well documented over large ranges of nutrient concentrations. Our study suggests that the nutrient response is suppressed by other controlling factors on the lower limb of the nutrient response curve (i.e. at low nutrient concentrations); a quantitatively significant response occurs only in excess of a threshold beyond which nutrients become dominant over other controlling factors. This interpretation of the results is consistent with published meta‐analyses showing lack of nutrient response for a high proportion of experimentally enriched periphyton communities, and division of responses between N and P for communities that do show growth in response to enrichment. 4. Grazing probably is not the key controlling variable for periphyton in Colorado mountain streams, given that the highest chlorophyll concentrations are associated with the highest abundances of macroinvertebrates. Modelling indicates that the initial amount of periphyton biomass at the start of the growing season, in conjunction with elevation‐related length of the growing season and water temperature, explains most of the variation in periphyton accumulation among these streams, but there is a yet unexplained suppression of periphyton growth rates across all elevations.     

Argali Abundance in the Afghan Pamir Using Capture–Recapture Modeling From Fecal DNA

Abstract: Estimating population size in a mark-recapture framework using DNA obtained from remotely collected genetic samples (e.g., feces) has become common in recent years but rarely has been used for ungulates. Using DNA extracted from fecal pellets, we estimated the size of an argali (Ovis ammon) population that was believed to be isolated from others within the Big Pamir Mountains, Afghanistan, an area where access was difficult and expensive. We used closed-capture models to estimate abundance, and Pradel models to examine closure assumptions, both as implemented in Program MARK. We also made visual counts of argali in the Big Pamirs, allowing comparison of count indices of abundance with modeled estimates. Our model-averaged estimate for female argali in the Big Pamir was 172 (95% CI = 117–232), which was about 23% higher than our best assessment using uncorrected visual counts. However, mark-recapture models suggested that males were not a closed population; thus, we were unable to provide a meaningful estimate of overall population size. Males either suffered much higher mortality than females during the sampling period, or, more likely, males moved in and out of the Big Pamir area. Although information from DNA did not provide a clear overall population estimate, it suggested that the Big Pamir was not isolated from other argali populations, which could not have been confirmed with visual observations alone. Estimating argali population size using mark-recapture models and fecal DNA is feasible but may be too expensive for frequent monitoring of large and remote populations. Our study demonstrates the importance of sex identification and separate abundance estimation for each sex, especially if movement ecology differs by sex.     

Survival and Breeding Transitions for a Reintroduced Bison Population: a Multistate Approach

Abstract: The iconic plains bison (Bison bison) have been reintroduced to many places in their former range, but there are few scientific data evaluating the success of these reintroductions or guiding the continued management of these populations. Relying on mark-recapture data, we used a multistate model to estimate bison survival and breeding transition probabilities while controlling for the recapture process. We tested hypotheses in these demographic parameters associated with age, sex, reproductive state, and environmental variables. We also estimated biological process variation in survival and breeding transition probabilities by factoring out sampling variation. The recapture rate of females and calves was high (0.78 ± 0.15 [SE]) and much lower for males (0.41 ± 0.23), especially older males (0.17 ± 0.15). We found that overall bison survival was high (>0.8) and that males (0.80 ± 0.13) survived at lower rates than females (0.94 ± 0.04), but as females aged survival declined (0.89 ± 0.05 for F ≥15 yr old). Lactating and non-lactating females survived at similar rates. We found that females can conceive early (approx. 1.5 yr of age) and had a high probability (approx. 0.8) of breeding in consecutive years, until age 13.5 years, when females that were non-lactating tended to stay in that state. Our results suggest senescence in reproduction and survival for females. We found little support for the effect of climatic covariates on demographic rates, perhaps because the park's current population management goals were predicated from drought-year conditions. This reintroduction has been successful, but continued culling actions will need to be employed and an adaptive management approach is warranted. Our demographic approach can be applied to other heavily managed large-ungulate systems with few or no natural predators.     

Identification of Compounds with Bioactivity against the Nematode Caenorhabditis elegans by a Screen Based on the Functional Genomics of the Marine Bacterium Pseudoalteromonas tunicata D2

Marine bacteria are a rich, yet underexplored, resource of compounds with inhibitory bioactivity against a range of eukaryotic target organisms. Identification of those inhibitors, however, requires a culturable or genetically tractable producer strain, a prerequisite that is not often fulfilled. This study describes a novel functional genomic screen that is based on expression of inhibitors in a heterogeneous recombinant host (i.e., Escherichia coli). Functional libraries were screened by selective grazing by the nematode Caenorhabditis elegans, in a simple, rapid, high-throughput manner. We applied our approach to discover inhibitors of C. elegans produced by the marine bacterium Pseudoalteromonas tunicata D2, a model organism for exploring a range of antagonistic activities between bacteria and eukaryotes and a known producer of several toxic compounds. Expression of P. tunicata DNA in E. coli and grazing selection by the nematode Caenorhabditis elegans identified two clones, with slow- and fast-killing modes of action. Genomic analysis of the slow-killing clone revealed that the activity was due to a small molecule, tambjamine, while the fast-killing activity involved a gene encoding for a novel protein. Microscopic analysis showed substantial colonization of the intestinal lumen, or rapid death of the nematode without colonization, for the two activities, respectively. The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions.Marine environments harbor highly diverse microbial communities, with an estimated more than one million different species (60). The vast majority of these are still functionally undescribed and unexplored, and only a fraction of the total number of species can currently be investigated by culture-dependent methods (47). Surface-associated marine microorganisms thrive in challenging habitats, often characterized by space and nutrient limitation, competition with other microorganisms, and colonizing higher organisms, as well as the targeted predation pressure by protozoa, nematodes, and other grazers. In response to this highly competitive environment, microorganisms have evolved strategies such as the production of toxins, attachment structures, biofilm formation, and host resilience in order to prevent the settlement and growth of competitive colonizers and for protection against bacterivorous predators. In fact, some of these adaptive traits are now recognized as virulence factors against a range of eukaryotic organisms, including plants, animals, and humans (24, 25, 44, 46). Despite this realization, there is limited information available on the presence and function of virulence factors in marine microbial organisms, nor is the full potential to mine such organisms for novel compounds with bioactivity realized.The marine bacterial genus Pseudoalteromonas contains numerous species, which synthesize biologically active molecules. Many of these species have been demonstrated to produce an array of low- and high-molecular-weight compounds with antimicrobial, algicidal, neurotoxic, and other pharmaceutically relevant activities (7). P. tunicata strain D2 is the most comprehensively studied species within the genus (7). This species colonizes sessile eukaryotes such as algae and tunicates and is a producer of several compounds with inhibitory activities against a range of organisms. Although the identity of several of these compounds remains to be elucidated, they target a range of bacteria, fungi, invertebrate larvae, diatoms, algal spores, and protozoa (15, 28, 29). Furthermore, a recent analysis of the P. tunicata D2 genome revealed properties characteristic of pathogens such as curli, several proteases, and homologs to virulence regulators (59). Hence, P. tunicata D2 is a powerful model system in which to investigate bioactive compounds and their mode of action, including those that serve as virulence factors.In order to detect and identify bacterial bioactive compounds that target multicellular eukaryotes, the nematode Caenorhabditis elegans can be utilized as a model system. This free-living worm provides several practical experimental advantages, including its ability to feed solely on bacteria, a short life cycle, and easy cultivation in large numbers. Comprehensive studies have reported the nematode as a versatile model metazoan in which to assess the virulence of many human, animal, plant, and insect pathogens (53). Some of the characteristics of the C. elegans immune system are conserved in higher eukaryotic organisms; moreover, diverse bacterial virulence factors necessary for killing of the nematode are used as virulence strategies regardless of the host (53). Despite the progress made using this model, current methods that help elucidate microbial genes involved in toxin-mediated killing or virulence are time-consuming or require expensive automation. Furthermore, a large fraction of potentially pathogenic bacteria elude investigations because they are not cultivable by using conventional laboratory techniques (47) or because of incompatible culture conditions for the pathogen and C. elegans (e.g., C. elegans is cultured at 25°C, while the Yersinia pestis virulence factors are upregulated only at 37°C [55]). Therefore, new high-resolution and simple methods are required to study genes and effector molecules mediating the inhibitory or toxic activity displayed by both cultured and uncultured bacteria.In the present study we investigate the presence and activity of toxins in P. tunicata D2 with a rapid, culture-independent, eukaryotic screening assay. Our novel approach is based on the ability of C. elegans, using a sophisticated chemosensory system, to perceive and behaviorally respond to a range of chemical cues, including deterrence from noxious substances and attraction to nutrients or signals (2, 4, 26, 27, 45, 51, 52, 61, 62). The high-throughput screen successfully detected antinematode bioactive compounds and rapidly identified the responsible P. tunicata D2 genes and gene products in a recombinant Escherichia coli clone library. To our knowledge, this is the first time that a functional genomic library screening has been used to identify antinematode bioactive compounds.     

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.     

Building and analyzing protein interactome networks by cross-species comparisons

Background  

A genomic catalogue of protein-protein interactions is a rich source of information, particularly for exploring the relationships between proteins. Numerous systems-wide and small-scale experiments have been conducted to identify interactions; however, our knowledge of all interactions for any one species is incomplete, and alternative means to expand these network maps is needed. We therefore took a comparative biology approach to predict protein-protein interactions across five species (human, mouse, fly, worm, and yeast) and developed InterologFinder for research biologists to easily navigate this data. We also developed a confidence score for interactions based on available experimental evidence and conservation across species.     

Using species distribution models to identify suitable areas for biofuel feedstock production

The 2007 Energy Independence and Security Act mandates a five‐fold increase in US biofuel production by 2022. Given this ambitious policy target, there is a need for spatially explicit estimates of landscape suitability for growing biofuel feedstocks. We developed a suitability modeling approach for two major US biofuel crops, corn (Zea mays) and switchgrass (Panicum virgatum), based upon the use of two presence‐only species distribution models (SDMs): maximum entropy (Maxent) and support vector machines (SVM). SDMs are commonly used for modeling animal and plant distributions in natural environments, but have rarely been used to develop landscape models for cultivated crops. AUC, Kappa, and correlation measures derived from test data indicate that SVM slightly outperformed Maxent in modeling US corn production, although both models produced significantly accurate results. When compared with results from a mechanistic switchgrass model recently developed by Oak Ridge National Laboratory (ORNL), SVM results showed higher correlation than Maxent results with models fit using county‐scale point inputs of switchgrass production derived from expert opinion estimates. However, Maxent results for an alternative switchgrass model developed with point inputs from research trial sites showed higher correlation to the ORNL model than the corresponding results obtained from SVM. Further analysis indicates that both modeling approaches were effective in predicting county‐scale increases in corn production from 2006 to 2007, a time period in which US corn production increased by 24%. We conclude that presence‐only methods are a powerful first‐cut tool for estimating relative land suitability across geographic regions in which candidate biofuel feedstocks can be grown, and may also provide important insight into potential land‐use change patterns likely to be associated with increased biofuel demand.