Pollen and fungal spore sampling and analysis. Statistical evaluations

Statistical evaluations of samples obtained from a Burkard seven-day recording volumetric pollen/spore trap were performed to determine the precision of the sampling and analysis procedures. The reproducibility of co-located traps was also investigated. The results showed that pollen grain transect counting was not significantly different, while fungal spore counting produced statistically different results. There was no statistical difference in the number of pollen and fungal spores counted between the co-located samplers. Reasons for the differences in the fungal spore counts are presented.     

iGibbs: improving Gibbs motif sampler for proteins by sequence clustering and iterative pattern sampling

The motif prediction problem is to predict short, conserved subsequences that are part of a family of sequences, and it is a very important biological problem. Gibbs is one of the first successful motif algorithms and it runs very fast compared with other algorithms, and its search behavior is based on the well-studied Gibbs random sampling. However, motif prediction is a very difficult problem and Gibbs may not predict true motifs in some cases. Thus, the authors explored a possibility of improving the prediction accuracy of Gibbs while retaining its fast runtime performance. In this paper, the authors considered Gibbs only for proteins, not for DNA binding sites. The authors have developed iGibbs, an integrated motif search framework for proteins that employs two previous techniques of their own: one for guiding motif search by clustering sequences and another by pattern refinement. These two techniques are combined to a new double clustering approach to guiding motif search. The unique feature of their framework is that users do not have to specify the number of motifs to be predicted when motifs occur in different subsets of the input sequences since it automatically clusters input sequences into clusters and predict motifs from the clusters. Tests on the PROSITE database show that their framework improved the prediction accuracy of Gibbs significantly. Compared with more exhaustive search methods like MEME, iGibbs predicted motifs more accurately and runs one order of magnitude faster.     

The importance of combining air sampling and surface analysis when studying problematic houses for mold biodiversity determination

Houses that underwent water damages are often responsible for heath problems of the occupants. Since there is no universally used protocol for the analysis, we wanted to verify the usefulness of surface sampling versus air sampling for the evaluation of mold diversity in problematic houses and the value of the number of visible mold growth zones to predict air quality. Seventeen houses were sampled for culturable molds in the air and on the surfaces showing contamination. We compared the mold taxa found in the air and on the surfaces and verified the correlation between the number of moldy surfaces and airbone mold concentration. This study demonstrated that, surprisingly, some of the so called wet spore molds (e.g. Stachybotrys) were found more often from air than surface samples whereas, some dry spore molds (e.g. Asp. fumigatus) was more easily isolated from surface samples. There was a good correlation between the number of visible mold growth zones and the concentration of airborne molds. We conclude that air and surface sampling are necessary to evaluate mold diversity in problematic houses and that the number of mold growth zones is a good predictor of airborne mold concentration.     

The efficiency of a new lightweight suction sampler for sampling aphids and their predators in arable land

A petrol driven machine, normally used to collect leaf litter, was modified to be used as a suction sampler for polyphagous predators in cereals and grassy habitats and aphids in cereals. Recovery efficiency of Araneae, Carabidae and Staphylinidae did not differ significantly between winter sampling from Agrostis stolonifera, Dactylis glomerata, Festuca rubra, Holcus lanatus or Lolium perenne although the structure of these grasses was very different. Summer sampling of aphids and their predators in winter wheat showed that the new sampler captured significantly more target organisms per unit area than did a traditional suction sampler. The machine was also lighter, cheaper and much easier to use than a traditional machine.     

Ranked set sampling for replicated sampling designs

In practical ecological sampling studies, a certain design (such as plot sampling or line-intercept sampling) is usually replicated more than once. For each replication, the Horvitz-Thompson estimation of the objective parameter is considered. Finally, an overall estimator is achieved by averaging the single Horvitz-Thompson estimators. Because the design replications are drawn independently and under the same conditions, the overall estimator is simply the sample mean of the Horvitz-Thompson estimators under simple random sampling. This procedure may be wisely improved by using ranked set sampling. Hence, we propose the replicated protocol under ranked set sampling, which gives rise to a more accurate estimation than the replicated protocol under simple random sampling.     

Airborne pollen in Kiev (Ukraine): Gravimetric sampling

This article presents the results of aeropalynological observations in Kiev, carried out with a gravimetric method, during January–October, 1994. The six most abundant pollen types were: Betulaceae (21%), Chenopodiaceae/Amaranthaceae (10%), Ambrosia (10%), Artemisia (9%) Pinaceae (8%) and Poaceae (6%). Seasonal fluctuations of the atmospheric presence of tree/shurb and herb/grass pollen during the period March–September, 1993 and 1994, are also shown.     

Airborne pollen in Kiev (Ukraine): gravimetric sampling

This article presents the results of aeropalynological observations in Kiev, carried out with a gravimetric method, during January–October, 1994. The six most abundant pollen types were: Betulaceae (21%), Chenopodiaceae/Amaranthaceae (10%), Ambrosia (10%), Artemisia (9%) Pinaceae (8%) and Poaceae (6%). Seasonal fluctuations of the atmospheric presence of tree/shrub and herb/grass pollen during the period March–September, 1993 and 1994, are also shown.     

Performance of the Coriolis air sampler,a high-volume aerosol-collection system for quantification of airborne spores and pollen grains

The Coriolis δ air sampler manufactured by Bertin Technologies (France) is a continuous air sampler, dedicated to outdoor monitoring of airborne spores and pollen grains. This high-volume sampler is based on patented Coriolis technology delivering a liquid sample. The air is drawn into a conical vial in a whirling type motion using suction; particles are pulled against the wall by centrifugal force. Airborne particles are separated from the air and collected in a liquid medium. This innovative solution allows rapid analysis by several techniques including PCR assay and serological assay in order to measure the antigenicity/allergenicity of pollen grains and fungal spores. Also, traditional counting of pollen grains or taxa identification by optical microscopy can be done. A study has been carried out by the Health Protection Agency (HPA), Porton Down, UK, to measure the physical efficiency of the Coriolis air sampler. The physical efficiency of the sampler for collection of micro-organism-laden particles of various sizes has been compared with that of membrane filter samplers using the techniques described by ISO 14698-1. The Coriolis was operated simultaneously with membrane filter samplers in a controlled room where they were challenged with uniform-sized particles of different diameters containing bacterial spores. For the larger particle sizes, it was found that the physical efficiency of the Coriolis was 92% for 10-μm particles. The biological performance of the Coriolis in the collection of airborne fungal spores and pollen grains was evaluated in comparison with a Hirst spore trap (one-week tape-on-drum type sampler) which is one of the most frequently used traps in the measurement of outdoor pollen grain concentrations. The advantages and limitations of both technologies are discussed. The Coriolis was operated simultaneously with a Hirst spore trap in the sampling station of Réseau National de Surveillance Aérobiologique, France (RNSA); the pollen grain and fungal spore counts were analysed by optical microscopy. The pollen grain count m⁻³ collected was compared for both devices. The dispersion values were obtained and statistical analysis was carried out. This study shows that the Coriolis air sampler provided equivalent recovery of pollen grain and fungal spores compared with the volumetric trap standard method (not significantly different, W test, α = 0.05). Nowadays, the French-led project, acronym MONALISA, with financial support from the European Commission––Life-Environment (LIFE05 ENV/F/000068), is testing this innovative air sampler in order to measure the antigenicity/allergenicity of the main aeroallergen particles, i.e. Betula (birch), Poaceae (grasses), Parietaria (pellitory), Olea spp (olive tree), and Artemisia (mugwort) pollen grains, and Alternaria (fungal spores) to validate a new approach of monitoring instead of quantifying pollen grains by their morphology. The robustness and efficiency of the MONALISA system is being demonstrated at a national level throughout Europe in eight different countries with different bio-climatic and topography characteristics: France, UK, Finland, Poland, Spain, Portugal, Switzerland, and Italy.     

A simple syringe sampler for sampling bottom waters

SUMMARY. A cheap messenger-operated device for sampling water immediately above sediment is described.     

A dispersal-limited sampling theory for species and alleles

The importance of dispersal for biodiversity has long been recognized. However, it was never advertised as vigorously as Stephen Hubbell did in the context of his neutral community theory. After his book appeared in 2001, several scientists have sought and found analytical expressions for the effect of dispersal limitation on community composition, still in the neutral context. This has been done along two relatively independent lines of research that have a different mathematical approach and focus on different, yet related, types of results. Here, we study both types in a new framework that makes use of the sampling nature of the theory. We present sampling distributions that contain binomial or hypergeometric sampling on the one hand, and dispersal limitation on the other, and thus views dispersal limitation as ubiquitous as sampling effects. Further, we express the results of one line of research in terms of the other and vice versa, using the concept of subsamples. A consequence of our findings is that metacommunity size does not independently affect the outcome of neutral models in contrast to a previous assertion (Ecol. Lett., 7, 2004, p. 904) based on an incorrect formula (Phys. Rev. E, 68, 2003, p. 061902, eqns 11-14). Our framework provides the basis for development of a dispersal-limited non-neutral community theory and applies in population genetics as well, where alleles and mutation play the roles of species and speciation respectively.     

Simple methods for sampling periphyton with observations on sampler design criteria

Requirements for an ideal standard sampling system for defined periphyton communities are discussed. Several simple and inexpensive devices for both spatially discrete and continuous sampling modes are described and field tested in a variety of habitats.     

Hand-operated box sampler for shallow water

The construction and operation of a hand-operated box sampler is described. The sampler covers an area of 25 × 25 cm and penetrates into the sediment to the depth of 15 cm. It was successfully operated on a sandy bottom, and on sand mixed with gravel up to a water depth of 1 meter.IAEC, Yavne 70600, Israel     

Fern spore and pollen airspora profile of Singapore

Monitoring atmospheric fern spore and pollen loads in Singapore was initiated in June 1990. Aside from the more numerous fungal spores, fern spores and pollen grains made up 6.2–8.6% and 4.4–5.4% of the total airspora sampled, respectively. The most frequently encountered fern spores, in descending order, were those of Nephrolepis auriculata, Dicranopteris linearis, Stenochlaena palustris, Asplenium nidus, Pteridium aquilinum, and Dicranopteris curranii. For pollen grains, the most frequently encountered, in descending order, were Elaeis guineensis, Casuarina equisetifolia, Acacia auriculiformis, Kyllingia polyphylla, Podocarpus, and Poaceae pollen grains. Seasonal patterns for individual fern spore or pollen types were discernible despite the relatively uniform tropical climate in Singapore. The fern spore and pollen calendar for the period 1991–1995 was compared to that of 2005–2006 as a follow-up study to keep abreast with the rapidly changing landscape of Singapore. Diurnal patterns showing a late morning to afternoon peak period were seen in fern spores, while the peak period was in the morning for pollen types studied with the exception to oil palm pollen. Additionally, association between fern spore and pollen counts and local meteorological conditions were also analyzed and found to be highly correlated. This study has thus identified the fern spores and pollen airspora components, and determined the calendars, as well as diurnal profiles of the Singapore airspora and provides invaluable information for allergy studies by highlighting the trigger sources present in the environment.     

Improved techniques for sampling complex pedigrees with the Gibbs sampler

Markov chain Monte Carlo (MCMC) methods have been widely used to overcome computational problems in linkage and segregation analyses. Many variants of this approach exist and are practiced; among the most popular is the Gibbs sampler. The Gibbs sampler is simple to implement but has (in its simplest form) mixing and reducibility problems; furthermore in order to initiate a Gibbs sampling chain we need a starting genotypic or allelic configuration which is consistent with the marker data in the pedigree and which has suitable weight in the joint distribution. We outline a procedure for finding such a configuration in pedigrees which have too many loci to allow for exact peeling. We also explain how this technique could be used to implement a blocking Gibbs sampler.     

A new adhesive for airborne pollen sampling

There is a spreading interest to establish networks of information exchange on aerobiological data in order to carry out comparative studies of the biological air content of different regions. For this kind of study, it is of primary importance that the methods used are being standardized. Since most national networks are now made of comparable Hirst-type samplers, the second most important factor to consider will be the efficiency of the adhesive used on the Melinex tape. In this study, we report conclusive results using a double-side self adhesive acrylic tape (Scotch 3M 9425). Our results show higher capture efficiency (+20%) for the 3M tape as compared to the glycerine/gelatine coating traditionally used in Montréal for the capture of airborne pollen on the Melinex tape of Hirst samplers.