Linkage mapping reveals sex-dimorphic map distances in a passerine bird

Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2-8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific recombination rates.     

The international standard for teicoplanin.

An international standard for teicoplanin has been established on the basis of a collaborative study. There were five participating laboratories in five countries. The activity of the contents of each ampoule of the international standard for teicoplanin is defined as 51,550 IU of teicoplanin.     

Toward an international standard for PCR-based detection of food-borne thermotolerant Campylobacters: validation in a multicenter collaborative trial

As part of a European research project, the performance of a PCR assay to detect food-borne thermotolerant campylobacters (Campylobacter jejuni, C. coli, and C. lari) was evaluated through an international collaborative trial involving 12 participating laboratories. DNA from 10 target and 8 nontarget strains was tested, and the results were reported as the presence of a positive signal after gel electrophoresis. The overall inclusivity (sensitivity) was 93.7%, and the exclusivity (specificity) was 100%. The results indicate that the assay can become an international standard and can be confidently applied in microbiological laboratories.     

Characterizing complex mixed-species bird flocks using an objective method for determining species participation

We developed sampling methods to characterize the participation of bird species in foraging flocks led by the Eastern Tufted Titmouse (Baeolophus bicolor) in North-central Florida during winter, because standard field methods, developed primarily for permanent resident Neotropical flocks, were intractable in our system. During January–February 2004 and November 2004–March 2005, we observed 55 mixed-species flocks, recorded 40 potential flocking species [mean of 12.4 species (SD = 3.8; range 3–20), 26.3 individuals (SD = 12.2; range 8–60), and 3.1 titmice (SD = 1.4; range 1–7), per flock]. Twenty-six species were observed frequently enough (>10% of observations) to be included in analyses. We paired 60-min flock observations with 10-min point counts conducted in locations used by flocks, but after flocks had moved more than 100 m away. This method yielded a measure of flocking propensity: the ratio of the number of individuals observed in the flock versus during the point count for each species. We used regression tree (RT) analysis to classify species into groupings according to their levels of flock participation, and to investigate relationships between flocking propensity and various environmental and social factors that we measured. Our analysis identified three clear species groups; “Nuclear/Regular Associate” (12 spp.; high/moderate), “Occasional Associate” (four spp.; moderate/low), and “Non-joiner/Accidental” (ten spp.; low/no flocking propensity). Groupings were similar to schemes produced via more time-intensive field methods. In order to contextualize grouping categories, we conducted a review of flocking group definitions and relevant autecological information (e.g., interspecific sociality) about our study species. We found this method to be useful for geographically extensive sampling of species’ participation in mixed-species flocks, despite high inter-flock variability in species composition and limited labor.     

Least-squares method for restriction mapping

A least-squares procedure has been developed to aid in deriving restriction-fragment maps once the order of cutsites has been determined. A computer program which carries out this method can be used to map either linear or circular molecules.     

Establishing a standard definition for child overweight and obesity worldwide: international survey

This study aimed to develop an internationally acceptable definition of child overweight and obesity, specifying the measurement, reference population, and age and sex specific cut off points. Data on body mass index (weight/height) were obtained from 6 large nationally representative cross sectional surveys on growth from Brazil, Great Britain, Hong Kong, the Netherlands, Singapore, and the US. The study included 97,876 males and 94,851 females from birth to 25 years of age. For each of the surveys, centile curves were drawn that at age 18 years passed through the widely used cut-off points of 25 and 30 kg/sq. m for adult weight and obesity. The resulting curves were averaged to provide age- and sex-specific cut-off points from 2 to 18 years. The proposed cut off points, which are less arbitrary and more internationally based than current alternatives, should help to provide internationally comparable prevalence rates of overweight and obesity in children.     

Viscometric determination of carboxymethylcellulase in standard international units

A direct theoretical approach is described for using viscometric data to determine standard units of carboxymethylcellulase as recommended by the Commission on Enzymes. Application of the theory showed that under suitably defined conditions calculated units were directly proportional to the quantity of enzyme used for assay. When the theory was applied to a kinetic analysis of enzyme action, a linear relationship was obtained from a Lineweaver-Burk plot and allowed the Michaelis-Menten constant to be readily calculated. The theory can also be modified so that relative though arbitrary enzyme units can be obtained from one simple calculation. The method should be applicable to other depolymerases that cleave their substrate randomly.     

A poor international standard for trap selectivity threatens carnivore conservation

Unintentional mortality of endangered carnivores due to non-selective trapping is important for conservation and warrants urgent attention. Currently, non-selective traps are being approved and used based on trap selectivity tests conducted according to International Organization for Standardization (ISO) guidelines. We review these guidelines and find them inadequate, because: (1) the ISO definition of selectivity does not account for relative abundance of target and non-target species and does not therefore meaningfully reflect selectivity; (2) the guidelines methodology at best quantifies relative selectivity of one trap against another, which is of limited use unless the control trap is known to have an acceptable level of absolute selectivity for the target species; (3) information on relative trap selectivity cannot simply be extrapolated elsewhere, unless species assemblage and relative species abundances are consistent. We demonstrate that the ISO definition of trap selectivity is only a simple capture proportion and therefore does not represent trap selectivity. ISO guidelines on trap selectivity should be reviewed to reflect particular ecological scenarios and we suggest how this might be done. Policy-makers, practitioners and researchers should interpret scientific results more cautiously. Trap approval decisions should be based on scientific evidence to avoid undermining the conservation of biodiversity.     

Toward a general chemical method for rapidly mapping multi-protein complexes

Ru(II)(bpy2)32+Cl2, ammonium persulfate, and visible light irradiation has been shown to rapidly and efficiently cross-link several interacting proteins. However, this methodology has not yet been used to map the architecture of large multi-protein complexes. In this study, this chemistry is applied to the crystallographically characterized yeast proteasome. The data obtained demonstrate both the method's increased generality and fidelity in comparison to traditional bifunctional cross-linking reagents, while also highlighting the future need for developing better analytical techniques to separate cross-linked products.     

Toward an international standard for PCR-based detection of food-borne thermotolerant Campylobacters: assay development and analytical validation

As part of a European research project (FOOD-PCR), we developed a standardized and robust PCR detection assay specific for the three most frequently reported food-borne pathogenic Campylobacter species, C. jejuni, C. coli, and C. lari. Fifteen published and unpublished PCR primers targeting the 16S rRNA gene were tested in all possible pairwise combinations, as well as two published primers targeting the 23S rRNA gene. A panel of 150 strains including target and nontarget strains was used in an in-house validation. Only one primer pair, OT1559 plus 18-1, was found to be selective. The inclusivity and exclusivity were 100 and 97%, respectively. In an attempt to find a thermostable DNA polymerase more resistant than Taq to PCR inhibitors present in chicken samples, three DNA polymerases were evaluated. The DNA polymerase Tth was not inhibited at a concentration of 2% (vol/vol) chicken carcass rinse, unlike both Taq DNA polymerase and DyNAzyme. Based on these results, Tth was selected as the most suitable enzyme for the assay. The standardized PCR test described shows potential for use in large-scale screening programs for food-borne Campylobacter species under the assay conditions specified.     

Determination of antithyroid antibodies by an immunoenzymatic method; an adaptation for expressing results in international units]

Solid phase immunoenzymatic methods (ELISA) have been developed for the determination of antithyroglbulin (ATG), antimicrosomal (AMc) and antimembrane (ATMA) antibodies in blood serum. The results have been expressed in international units (IU). The level of nonspecific reaction was determined on the basis of 30 samples of blood serum obtained from healthy donors. The double standard deviation values amounted to 8 IU for antithyroglobulin antibodies, 17 IU for antimicrosomal antibodies and 53 IU for antimembrane antibodies at the serum dilution of 1:100. The values of double standard deviation obtained for the healthy donors correspond to the borderline between the positive serum samples and those containing no autoantibodies. The level of autoantibodies in patients with autoimmune diseases of the thyroid varied considerably ranging from complete absence to several thousand units per milliliter in single cases. Antithyroglobulin antibodies were determined simultaneously by using the described method and the commercial kit (Walker, Cambridge) and the results obtained by the two methods were compared. A linear correlation with the correlation coefficient r = 0.93, p < 0.001 was obtained. A good but nonlinear correlation was demonstrated with the methods expressing the results in titre values.     

Large body size in an island-dwelling bird: a microevolutionary analysis

Island races of passerine birds display repeated evolution towards larger body size compared with their continental ancestors. The Capricorn silvereye (Zosterops lateralis chlorocephalus) has become up to six phenotypic standard deviations bigger in several morphological measures since colonization of an island approximately 4000 years ago. We estimated the genetic variance-covariance (G) matrix using full-sib and 'animal model' analyses, and selection gradients, for six morphological traits under field conditions in three consecutive cohorts of nestlings. Significant levels of genetic variance were found for all traits. Significant directional selection was detected for wing and tail lengths in one year and quadratic selection on culmen depth in another year. Although selection gradients on many traits were negative, the predicted evolutionary response to selection of these traits for all cohorts was uniformly positive. These results indicate that the G matrix and predicted evolutionary responses are consistent with those of a population evolving in the manner observed in the island passerine trend, that is, towards larger body size.     

Multicenter validation of the analytical accuracy of Salmonella PCR: towards an international standard

As part of a major international project for the validation and standardization of PCR for detection of five major food-borne pathogens, four primer sets specific for Salmonella species were evaluated in-house for their analytical accuracy (selectivity and detection limit) in identifying 43 Salmonella spp. and 47 non-Salmonella strains. The most selective primer set was found to be 139-141 (K. Rahn, S. A. De Grandis, R. C. Clarke, S. A. McEwen, J. E. Galán, C. Ginocchio, R. Curtiss III, and C. L. Gyles, Mol. Cell. Probes 6:271-279, 1992), which targets the invA gene. An extended determination of selectivity by using 364 strains showed that the inclusivity was 99.6% and the exclusivity was 100% for the invA primer set. To indicate possible PCR inhibitors derived from the sample DNA, an internal amplification control (IAC), which was coamplified with the invA target gene, was constructed. In the presence of 300 DNA copies of the IAC, the detection probability for primer set 139-141 was found to be 100% when a cell suspension containing 10(4) CFU/ml was used as the template in the PCR (50 CFU per reaction). The primer set was further validated in an international collaborative study that included 16 participating laboratories. Analysis with 28 coded ("blind") DNA samples revealed an analytical accuracy of 98%. Thus, a simple PCR assay that is specific for Salmonella spp. and amplifies a chromosomal DNA fragment detected by gel electrophoresis was established through extensive validation and is proposed as an international standard. This study addresses the increasing demand of quality assurance laboratories for standard diagnostic methods and presents findings that can facilitate the international comparison and exchange of epidemiological data.     

Social networks and ornithology studies: an innovative method for rapidly accessing data on conspicuous bird species

We developed an innovative method for finding individuals of a conspicuous species in complex urban habitats. The aim of this study was to detect as many burrowing owl nests as possible in order to develop an ecological and behavioral study. We performed an online survey through the social network, Facebook. The results of this survey allowed us to detect and locate 36 new burrowing owl nests. We conclude that developing online surveys through social networks is an innovative and cost-effective method to obtain information about bird locations, and can complement traditional methods such as field surveys.     

Migratory restlessness in an equatorial nonmigratory bird

The urge of captive birds to migrate manifests itself in seasonally occurring restlessness, termed “Zugunruhe.” Key insights into migration and an endogenous basis of behavior are based on Zugunruhe of migrants but have scarcely been tested in nonmigratory birds. We recorded Zugunruhe of African stonechats, small passerine birds that defend year-round territories and have diverged from northern migrants at least 1 million years ago. We demonstrate that Zugunruhe is a regular feature of their endogenous program, one that is precisely timed by photoperiod. These results extend ideas of programs for periodic movement to include nonmigratory birds. Such programs could be activated when movements become necessary, in line with observed fast changes and high flexibility of migration. Attention to Zugunruhe of resident birds promises new insights into diverse and dynamic migration systems and enhances predictions of avian responses to global change.     

Methodological problems related to spotlight count as a census technique for Lepus europaeus in an alpine environment

Population estimations are necessary for effective conservation management. In Italy, brown hare populations are commonly censused by spotlighting, but this method does not seem to suit an alpine environment due to its vegetational and orographical complexity. The aim of this study is to evaluate the critical aspects related to spotlight census method in an alpine environment. Spotlight was carried out along two transects of a typical alpine environment. Observed animals were used to define density (number of animal seen/100 ha) and method precision (coefficient of variation (CV) applied to monthly repeated observations). Animal detectability was evaluated using half-normal function with cosine expansion (Distance 5.0®). Animal observability was evaluated by analyzing density estimates related to habitat conformation (unseen areas or full visibility). The exact surface surveyed by spotlighting was evaluated, defining the observation spotlight beam range (OTA) and the land useful sighting (LUS). In the end, LUS was classified in three patches according to hare presence: no hares, occasional hare presence, and constant hare presence. To evaluate habitat influence onto CV, we used a bootstrap simulation. The results show that spotlighting alone is not the most suitable method to apply in the alpine environment because habitat structure highly influences census results. Recommendations to improve spotlight surveys for monitoring European brown hare populations are given.