An ecological example of the application of projection pursuit to compositional data

A modern statistical technique for the exploratory analysis of multivariate data, called projection pursuit, is described. The method consists of the extraction and display of informative one- or two-dimensional projections of the multivariate dataset. Projection pursuit has much scope for application to ecological datasets. The example in this paper concerns element concentrations in soil samples from a coastal embayment on the east coast of Australia. The application attempts to search for patterns in the soils which could be related to vegetation patterns. The compositional nature of the dataset adds a novel element to the methodology.     

Factors affecting the abundance of introduced hedgehogs (Erinaceus europaeus) to the Hebridean island of South Uist in the absence of natural predators and implications for nesting birds

Introduced hedgehogs Erinaceus europaeus are a known threat to ground-nesting birds on many islands. Spring hedgehog density and sex ratio were measured over a 5-year period at four plots on the 315 km² Hebridean island of South Uist. The mean instantaneous density on the sandy-soiled machair plots (31.8 hedgehogs km⁻², se 2.95) was over twice that on the peaty-soiled blackland plots (15.4 hedgehogs km⁻², se 3.46), a difference reflecting the amount of preferred foraging habitat (mainly pasture). Plot population densities fluctuated approximately in unison. Year-to-year density changes were strongly correlated with temperature in the preceding winter and previous year's spring/summer, indicating that warmer conditions promote both survival and breeding success. The mean spring sex ratio of sub-adults (animals born in the previous calendar year) was not significantly different from 1M:1F. However, the 1.8M:1F ratio observed for adults was significantly male biased, probably a result of female mortality associated with rearing young. The study estimates that in an average year the South Uist hedgehog population numbers c . 2750 (95% confidence limit±800) adults and sub-adults and these produce around 3000 young. Compared with the native range, hedgehog densities on South Uist are shown to be unusually high, probably because their natural predators are absent. High hedgehog densities have led directly to high rates of egg predation of ground-nesting shorebirds and subsequent declines in bird populations. The results suggest that over the past 20 years egg losses have become more severe and control of hedgehogs more difficult because climate warming has resulted in generally more favourable conditions for hedgehogs on the islands.     

Antimicrobial activity of lipoprotein particles containing apolipoprotein Al

Human plasmain vitro inhibits the growth of coagulase negative staphylococci,S. epidermidis, which may be pathogenic in the immunocompromised host. To determine the antimicrobial components, serum was fractionated by column chromatography, which revealed that elution areas where lipoproteins can be yielded had high antimicrobial activity againstS. epidermidis. Therefore, lipoprotein fractions, including very low density lipoprotein (VLDL), low density lipoprotein (LDL) and high density lipoprotein (HDL), were separated by ultracentrifugation and incubated withS. epidermidis. All 3 lipoprotein fractions suppressed bacterial growth within the first 3 h but VLDL enhanced bacterial growth after 9 h of incubation compared with the control. HDL, however, inhibited bacterial growth throughout 21 h of incubation.To confirm these results, serum from healthy volunteers was separated by ion exchange column chromatography and again by HPLC to purify the antimicrobial fraction. In the protein analysis with gradient polyacrylamide-SDS gel, apolipoprotein Al (apo Al), which is a major apolipoprotein of HDL, was detected in the antimicrobial fraction. Therefore, this fraction was loaded onto an immunoaffinity column coupled with the anti-apo Al monoclonal antibody (Mab). Unbound fraction had no antimicrobial activity, but anti-S. epidermidis activity was recovered from the bound fraction which consisted mainly of apo Al, All and apo C in protein composition.These results indicated that the antimicrobial activity was associated with the apo Al-containing lipoprotein particles (HDL). This property of HDL may directly affect bacterial growth and promote the self-defense mechanisms of normal and immunocompromised individuals.     

Separation and analysis of cell types involved in early stages of carrot somatic embryogenesis

The occurrence of the polarized synthesis of DNA in embryogenic cell clusters of carrot on the third and fourth days after transfer to an embryogenesis-inducing medium was observed by labeling with [³H]thymidine and autoradiography. The cells that were actively synthesizing DNA were separated from cells that were not synthesizing DNA by maceration of cell clusters into individual protoplasts and centrifugation in a Percoll density gradient. [³⁵S]Methionine-labeled proteins extracted from the two types of cell were analyzed by SDS-PAGE and fluorography. Three polypeptides (of 69, 98 and 108 kD, respectively) were found only in cells that were actively synthesizing DNA and could be candidates for markers of the polarity of DNA synthesis that is specific to embryogenesis.     

Variation in recombination rate may bias human genetic disease mapping studies

The availability of the human genome sequence and variability information (as from the International HapMap project) will enhance our ability to map genetic disorders and choose targets for therapeutic intervention. However, several factors, such as regional variation in recombination rate, can bias conclusions from genetic mapping studies. Here, we examine the impact of regional variation in recombination rate across the human genome. Through computer simulations and literature surveys, we conclude that genetic disorders have been mapped to regions of low recombination more often than expected if such diseases were randomly distributed across the genome. This concentration in low recombination regions may be an artifact, and disorders appearing to be caused by a few genes of large effect may be polygenic. Future genetic mapping studies should be conscious of this potential complication by noting the regional recombination rate of regions implicated in diseases.     

A flow injection analysis system with encapsulated high-density <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> cells for rapid determination of biochemical oxygen demand

The biochemical oxygen demand (BOD) determination was studied using a novel flow injection analysis (FIA) system with encapsulated Saccharomyces cerevisiae cells and an oxygen electrode and was compared with conventional 5-day BOD tests. S. cerevisiae cells were packed in a calcium alginate capsule at a dry cell weight of 250 g/l of capsule core. The level of dissolved oxygen (DO) was reduced due to the enhanced respiratory activity of the microbial cells when the injected nutrient passed through the bioreactor. The decrease in DO (ΔDO) was intensified with the amount of microbial cells packed in the bioreactor. However, the specific ΔDO decreased as the amount of cells loaded in the bioreactor increased. The ΔDO value was dependent on the pH and temperature of the mobile phase and reached its maximum value at 35°C and pH 7–8. Also, ΔDO became larger at longer response times as the flow rate of the mobile phase decreased. The measurement of ΔDO was repeated more than six times consecutively using a 20-ppm standard glucose and glutamic acid solution, which confirmed the reproducibility with a standard deviation of 0.95%. A strong linear correlation between ΔDO and BOD was also observed. The 5-day BOD values of actual water and wastewater samples were in accordance with the BOD values obtained by this FIA method using encapsulated S. cerevisiae cells. Unlike the cell-immobilized bead system, there was no contamination of the bioreactor resulting from any leak of yeast cells from the sensor capsules during BOD measurements.     

The effects of nutrient enrichment on a freshwater meiofaunal assemblage

1. The effects of eutrophication on phytoplankton, zooplankton and fish in lakes are well known. By contrast, little is known about the response of the zoobenthos to nutrient enrichment, while smaller organisms, such as the meiofauna, have for the most part been neglected. 2. In a long‐term (16 months) microcosm experiment, we assessed the effects of five levels of nutrients [total phosphorus (TP), 7–250 μg L^?1; nitrate, 2–8 mg L^?1] on a freshwater meiofaunal assemblage and on nematode diversity in particular. 3. Within the first 8 months, meiofaunal succession was only weakly affected, whereas, during the last 4 months, nutrient addition influenced most of the main taxa, with a concomitant change in the assemblage structure. 4. The density of the numerically dominant nematodes decreased upon nutrient enrichment, whereas ostracods became more numerous. Other taxa, including copepods, reached a maximum at intermediate nutrient levels or, in case of oligochaetes, were almost unaffected by nutrient enrichment. However, the changes in the density of the main taxa were usually insufficient to alter their biomass. Consequently, meiofaunal biomass was remarkably unresponsive to nutrient addition, while meiofaunal density displayed a unimodal relationship, with a peak at a TP concentration of 30 μg L^?1. In addition, nematode species richness decreased significantly with increasing nutrient concentrations. 5. We hypothesise that the response of meiofaunal taxa to nutrients is attributable to the development of primary producers, which shifted with enrichment from low densities of edible diatoms and unicellular green algae to large standing stocks of inedible forms, such as Lemna minor and Cladophora spp.     

Laboratory culture of Chironomus tentans for use in toxicity testing: optimum initial egg-stocking densities

The midge Chironomus tentans Fabricius is a commonly used freshwater invertebrate in sediment toxicity tests. Rigorous laboratory culturing techniques are needed to provide organisms of uniform quality and known age for use in testing and for the continuation of the culture itself. This study was conducted to determine the effect of initial culture stocking density on: (1) post-hatch (larval) dry weight, body length and head-capsule width at 10 and 20 days; (2) time to emergence; (3) number and sex of emergent adults; (4) number of larvae and pupae at test termination (day 42 post hatch); and (5) adult dry weight. Three egg stocking densities were used 690 (1.1 eggs cm^–2), 1043 (1.7 eggs cm^–2) and 1463 (2.4 eggs cm^–2). Mean weight of larvae at 10 days in high density tanks (0.13 mg/organism) was significantly higher (P=0.003) than both the medium and low density tanks (0.10 and 0.09 mg/organism, respectively). No significant differences between the three stocking densities were observed for the body length or head-capsule width at either 10 or 20 days post-hatch. Although not statistically significant, larval dry weight decreased with increased stocking density at day 20. A significantly (P=0.02) greater number of females (173±28) emerged from the low stocking density compared to both the medium and high stocking densities (123±45 and 118±54, respectively). Peak adult emergence for the low and medium stocking densities occurred between days 22 and 25 post-hatch, whereas peak adult emergence occurred between days 30 and 33 for the high stocking density. Survival relative to the initial number of eggs stocked was significantly greater (P=0.007) in the low density treatment compared to that in either the medium or the high density treatments. Mean adult weight exhibited an inverse relationship with initial stocking densities. At test end, there was not a significant difference in the mean number of organisms surviving and emerging in the three density levels. The central tendency for number of organisms surviving for all three treatments was 504 organisms per tank (0.82 organisms cm^–2). The results of this experiment suggest that an optimal egg stocking density of 1.0 egg cm^–2 (600 eggs/tank) be used with the feeding rate identified. This would ensure uniform larvae at the appropriate developmental stage (2nd–3rd instar) needed for toxicological research/testing (e.g. 10 days post-hatch), as well as producing sufficient emergence of males and females for future culture establishment.     

Model‐based high cell density cultivation of Rhodospirillum rubrum under respiratory dark conditions

The potential of facultative photosynthetic bacteria as producers of photosynthetic pigments, vitamins, coenzymes and other valuable products has been recognized for decades. However, mass cultivation under photosynthetic conditions is generally inefficient due to the inevitable limitation of light supply when cell densities become very high. The previous development of a new cultivation process for maximal expression of photosynthetic genes under semi‐aerobic dark conditions in common bioreactors offers a new perspective for utilizing the facultative photosynthetic bacterium Rhodospirillum rubrum for large‐scale applications. Based on this cultivation system, the present study aimed in determining the maximal achievable cell density of R. rubrum in a bioreactor, thereby providing a major milestone on the way to industrial bioprocesses. As a starting point, we focus on aerobic growth due to higher growth rates and more facile process control under this condition, with the option to extend the process by an anaerobic production phase. Process design and optimization were supported by an unstructured computational process model, based on mixed‐substrate kinetics. Key parameters for growth and process control were determined in shake‐flask experiments or estimated by simulation studies. For fed‐batch cultivation, a computer‐controlled exponential feed algorithm in combination with a pH‐stat element was implemented. As a result, a maximal cell density of 59 g cell dry weight (CDW) L^?1 was obtained, representing so far not attainable cell densities for photosynthetic bacteria. The applied exponential fed‐batch methodology therefore enters a range which is commonly employed for industrial applications with microbial cells. The biochemical analysis of high cell density cultures revealed metabolic imbalances, such as the accumulation and excretion of tetrapyrrole intermediates of the bacteriochlorophyll biosynthetic pathway. Biotechnol. Bioeng. 2010. 105: 729–739. © 2009 Wiley Periodicals, Inc.