Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Background  

Mass spectrometry for biological data analysis is an active field of research, providing an efficient way of high-throughput proteome screening. A popular variant of mass spectrometry is SELDI, which is often used to measure sample populations with the goal of developing (clinical) classifiers. Unfortunately, not only is the data resulting from such measurements quite noisy, variance between replicate measurements of the same sample can be high as well. Normalisation of spectra can greatly reduce the effect of this technical variance and further improve the quality and interpretability of the data. However, it is unclear which normalisation method yields the most informative result.     

Human activities link fruit bat presence to Ebola virus disease outbreaks

1. A significant link between forest loss and fragmentation and outbreaks of Ebola virus disease (EVD) in humans has been documented. Deforestation may alter the natural circulation of viruses and change the composition, abundance, behaviour and possibly viral exposure of reservoir species. This in turn might increase contact between infected animals and humans.
2. Fruit bats of the family Pteropodidae have been suspected as reservoirs of the Ebola virus. At present, the only evidence associating fruit bats with EVD is the presence of seropositive individuals in eight species and polymerase chain reaction-positive individuals in three of these.
3. Our study investigates whether human activities can increase African fruit bat geographical ranges and whether this influence overlaps geographically with EVD outbreaks that, in turn, are favoured by deforestation.
4. We use species observation records for the 20 fruit bat species found in favourable areas for the Ebola virus to determine factors affecting the bats' range inside the predicted Ebola virus area. We do this by employing a hypothetico-deductive approach based on favourability modelling.
5. We show that the range of some fruit bat species is linked to human activities within the favourable areas for the Ebola virus. More specifically, the areas where human activities favour the presence of five fruit bat species overlap with the areas where EVD outbreaks in humans were themselves favoured by deforestation. These five species are as follows: Eidolon helvum, Epomops franqueti, Megaloglossus woermanni, Micropteropus pusillus and Rousettus aegyptiacus. Of these five, all but Megaloglossus woermanni have recorded seropositive individuals. For the remaining 15 bat species, we found no biogeographical support for the hypothesis that positive human influence on fruit bats could be associated with EVD outbreaks in deforested areas within the tropical forest biome in West and Central Africa.
6. Our work is a useful first step allowing further investigation of the networks and pathways that may lead to an EVD outbreak. The modelling framework we employ here can be used for other emerging infectious diseases.

     

A general analysis of resource allocation by competing individuals.

A linear model for population dynamics in a stationary stochastic environment is introduced based on linearizing the N-species Lotka-Volterra competition equations in discrete time. Iteration of the linear model shows the sequence of population sizes to be formed from a simple linear operation on the sequence of carrying capacities. The transfer function for this operation is calculated and the spectral properties of time series data on population size follow directly.The above approach is illustrated with a symmetrical two-species competition system assuming white noise variation in the carrying capacities. The results are interpreted in detail with the following ideas. (1) The intrinsic rate of increase governs the “responsiveness” of the population to changes in the carrying capacity; (2) one effect of competition is to reduce the “effective rate of increase” of the population. Increasing competition can produce effects identical to that of lowering the intrinsic rate of increase; (3) the other effect of competition is to communicate the stochastic variation in one species' carrying capacity to its competitors. The end result of this communication depends critically on the cross-correlation scheme among the carrying capacities of the competing species.     

Spatial Distribution of Dorylaimid and Mononchid Nematodes from Southeast Iberian Peninsula: Chorological Relationships among Species

The spatial distribution of 138 Dorylaimid and Mononchid species collected in a natural area from the Southeast Iberian Peninsula was studied. A chorological classification was used to examine distribution patterns shared by groups of species. Eighty species were classified into 14 collective and 16 individual chorotypes. The geographical projections of several collective chorotypes are illustrated along with their corresponding distribution maps. The importance of this analysis to nematological study is briefly discussed.     

Factors influencing the distribution of chironomids and oligochaetes in profundal areas of Spanish reservoirs

A canonical correlation analysis was performed in order to explain the distribution and abundance of the profundal macrozoobenthos in 71 Spanish reservoirs. Two sets of variables were considered: one set consisted of subgroups of benthic organisms based on their feeding strategy, and the other consisted of environmental variables related to the trophic state of the reservoir.The results showed that densities of phytophagous chironomids decreased with water depth and increased with oxygen content in the bottom waters, while Tanypodinae densities increased with rising densities of phytophagous chironomids and/or oligochaetes, revealing their strong dependence on the abundance of available prey. The abundance of oligochaetes and phytophagous chironomids showed a disjunct distribution with season and depth, suggesting the importance of food quality and sediment texture.Oxygen availability and water depth acted as governing factors for the zoobenthos. Chlorophyll-a was of secondary importance and correlated inversely with the abundance of benthic fauna, especially in summer. Autogenic production coupled with inputs of allochthonous coarse particulate organic matter and a long stratification period lead to long lasting anoxia that reduces the benthic fauna in Spanish reservoirs.Only up to 18% of the variability in the biological data could be associated with the environmental factors considered. Thus, factors other than the trophic state are much more important in reservoirs. Fluctuations of the water level and inputs of organic and inorganic materials coming from the basin are greater than in lakes and act as stressing factors for the benthic fauna.     

Chironomids and regional water types

The distribution pattern of 115 chironomid taxa at 664 sites, distributed over all kinds of water, was analyzed and related to 42 water types, based on the complete macrofauna composition. The distinction of chironomid groups was not useful to recognize water types. The use of individual chironomid taxa was more sensitive, though also too limited to recognize water types clearly. Chironomids are distributed along a continuum which is directed by master factors and detailed by habitat factors.     

HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data

Background  

Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with increased signal intensity (as a result of hybridization of labeled DNA) in a region. Currently, no standard criteria are available to define these regions-of-interest as there is no single probe intensity cut-off level, different regions-of-interest can contain various numbers of probes, and can vary in genomic width. Furthermore, the chromosomal distance between neighboring probes can vary across the genome among different arrays.     

Biological activity ofTreponema hyodysenteriae hemolysin

The biological properties ofTreponema hyodysenteriae hemolysin (TH), which in some aspects resembles streptolysin S, were studied. Aside from different erythrocyte species, TH had no lytic activity on prokaryotic (protoplasts and spheroplasts) and eukaryotic (Chinese hamster ovary and spleen) cells. However, TH decreased the response of spleen cells to concanavalin A and lipopolysaccharide. In vivo, TH was found to induce fluid accumulation in ligated rat ileal loops as well as histological modifications similar to those observed in the swine dysentery. These results further differentiate TH from streptolysin S, and suggest that it is a new oxygen-resistant hemolysin produced by a Gram-negative bacterium.