Genetic variation in the cellular response of Daphnia magna (Crustacea: Cladocera) to its bacterial parasite

Linking measures of immune function with infection, and ultimately, host and parasite fitness is a major goal in the field of ecological immunology. In this study, we tested for the presence and timing of a cellular immune response in the crustacean Daphnia magna following exposure to its sterilizing endoparasite Pasteuria ramosa. We found that D. magna possesses two cell types circulating in the haemolymph: a spherical one, which we call a granulocyte and an irregular-shaped amoeboid cell first described by Metchnikoff over 125 years ago. Daphnia magna mounts a strong cellular response (of the amoeboid cells) just a few hours after parasite exposure. We further tested for, and found, considerable genetic variation for the magnitude of this cellular response. These data fostered a heuristic model of resistance in this naturally coevolving host–parasite interaction. Specifically, the strongest cellular responses were found in the most susceptible hosts, indicating resistance is not always borne from a response that destroys invading parasites, but rather stems from mechanisms that prevent their initial entry. Thus, D. magna may have a two-stage defence—a genetically determined barrier to parasite establishment and a cellular response once establishment has begun

Introduced birds in urban remnant vegetation : does remnant size really matter?

Introduced birds are a pervasive and dominant element of urban ecosystems. We examined the richness and relative abundance of introduced bird species in small (1&ndash;5 ha) medium (6&ndash;15 ha) and large (&gt;15 ha) remnants of native vegetation within an urban matrix. Transects were surveyed during breeding and non-breeding seasons. There was a significant relationship between introduced species richness and remnant size with larger remnants supporting more introduced species. There was no significant difference in relative abundance of introduced species in remnants of different sizes. Introduced species, as a proportion of the relative abundance of the total avifauna (native and introduced species), did not vary significantly between remnants of differing sizes. There were significant differences in the composition of introduced bird species between the different remnant sizes, with large remnants supporting significantly different assemblages than medium and small remnants. Other variables also have substantial effects on the abundance of introduced bird species. The lack of significant differences in abundance between remnant sizes suggests they were all equally susceptible to invasion. No patches in the urban matrix are likely to be unaffected by introduced species. The effective long-term control of introduced bird species is difficult and resources may be better spent managing habitat in a way which renders it less suitable for introduced species (e.g. reducing areas of disturbed ground and weed dominated areas).<br /

Parallel classification and feature selection in microarray data using SPRINT

The statistical language R is favoured by many biostatisticians for processing microarray data. In recent times, the quantity of data that can be obtained in experiments has risen significantly, making previously fast analyses time consuming or even not possible at all with the existing software infrastructure. High performance computing (HPC) systems offer a solution to these problems but at the expense of increased complexity for the end user. The Simple Parallel R Interface is a library for R that aims to reduce the complexity of using HPC systems by providing biostatisticians with drop‐in parallelised replacements of existing R functions. In this paper we describe parallel implementations of two popular techniques: exploratory clustering analyses using the random forest classifier and feature selection through identification of differentially expressed genes using the rank product method

Subchronic Exposure to TCDD, PeCDF, PCB126, and PCB153: Effect on Hepatic Gene Expression

We employed DNA microarray to identify unique hepatic gene expression patterns associated with subchronic exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other halogenated aromatic hydrocarbons (HAHs). Female Harlan Sprague-Dawley rats were exposed for 13 weeks to toxicologically equivalent doses of four different HAHs based on the toxic equivalency factor of each chemical: TCDD (100 ng/kg/day), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF; 200 ng/kg/day), 3,3′,4,4′,5-pentachlorobiphenyl (PCB126; 1,000 ng/kg/day), or 2,2′,4,4′,5,5′-hexachlorobiphenyl (PCB153; 1,000 μg/kg/day). Global gene expression profiles for each exposure, which account for 8,799 gene probe sets contained on Affymetrix RGU34A GeneChips, were compared by principal components analysis. The aryl hydrocarbon receptor (AhR) ligands TCDD, PeCDF, and PCB126 produced very similar global gene expression profiles that were unique from the nonAhR ligand PCB153, underscoring the extensive impact of AhR activation and/or the resulting hepatic injury on global gene expression in female rat liver. Many genes were co-expressed during the 13-week TCDD, PeCDF, or PCB126 exposures, including classical AhR-regulated genes and some genes not previously characterized as being AhR regulated, such as carcinoembryonic-cell adhesion molecule 4 (C-CAM4) and adenylate cyclase-associated protein 2 (CAP2). Real-time reverse-transcriptase polymerase chain reaction confirmed the increased expression of these genes in TCDD-, PeCDF-, and PCB126-exposed rats as well as the up- or down-regulation of several other novel dioxin-responsive genes. In summary, DNA microarray successfully identified dioxin-responsive genes expressed after exposure to AhR ligands (TCDD, PeCDF, PCB126) but not after exposure to the non-AhR ligand PCB153. Together, these findings may help to elucidate some of the fundamental features of dioxin toxicity and may further clarify the biologic role of the AhR signaling pathway

Where Does the Alignment Score Distribution Shape Come from?

Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number of times biologists face this class of distributions raises the question of the evolutionary origin of this probability law

Conditional Sampling for Max-Stable Processes with a Mixed Moving Maxima Representation

This paper deals with the question of conditional sampling and prediction for the class of stationary max-stable processes which allow for a mixed moving maxima representation. We develop an exact procedure for conditional sampling using the Poisson point process structure of such processes. For explicit calculations we restrict ourselves to the one-dimensional case and use a finite number of shape functions satisfying some regularity conditions. For more general shape functions approximation techniques are presented. Our algorithm is applied to the Smith process and the Brown-Resnick process. Finally, we compare our computational results to other approaches. Here, the algorithm for Gaussian processes with transformed marginals turns out to be surprisingly competitive.Comment: 35 pages; version accepted for publication in Extremes. The final publication is available at http://link.springer.co

Up-regulation of Tissue Factor in Human Pulmonary Artery Endothelial Cells after Ultrafine Particle Exposure

BACKGROUND: Epidemiology studies have linked exposure to pollutant particles to increased cardiovascular mortality and morbidity, but the mechanisms remain unknown. OBJECTIVES: We tested the hypothesis that the ultrafine fraction of ambient pollutant particles would cause endothelial cell dysfunction. METHODS: We profiled gene expression of human pulmonary artery endothelial cells (HPAEC) exposed to ultrafine particles (UFPs; 100 μg/mL) from Chapel Hill, North Carolina, or vehicle for 4 hr with Affymetrix HG U133 Plus 2.0 chips (n = 4 each). RESULTS: We found 320 up-regulated genes and 106 down-regulated genes (p < 0.01, 5% false discovery rate). We noted up-regulation of genes related to coagulation [tissue factor (F3) and coagulation factor II receptor-like 2 (F2RL2)] and differential regulation of genes related to F3 signaling (FOS, JUN, and NFKBIA). Results of quantitative polymerase chain reaction show a significant up-regulation of F3 after 10 and 100 μg/mL UFP exposures. Additionally, the water-soluble fractions of UFPs were sufficient to induce the expression of F3, F2RL2, and heme oxygenase 1 (HMOX1). Treatment of HPAEC with UFPs for 16 hr increased the release of interleukin (IL)-6 and IL-8. Pretreatment of HPAEC with a blocking antibody against F3 attenuated IL-6 and IL-8 release by 30 and 70%, respectively. CONCLUSIONS: Using gene profiling, we discovered that UFPs may induce vascular endothelial cells to express genes related to clotting. These results indicate that PM may cause adverse cardiovascular health effects by activating coagulation-inflammation circuitry

Mycobacterium bovis shedding patterns from experimentally infected calves and the effect of concurrent infection with bovine viral diarrhoea virus

Concurrent infection of cattle with bovine viral diarrhoea virus (BVDV) and Mycobacterium bovis is considered to be a possible risk factor for onward transmission of bovine tuberculosis (BTB) in infected cattle and is known to compromise diagnostic tests. A comparison is made here of M. bovis shedding (i.e. release) characteristics from 12 calves, six experimentally co-infected with BVDV and six infected with M. bovis alone, using simple models of bacterial replication. These statistical and mathematical models account for the intermittent or episodic nature of shedding, the dynamics of within-host bacterial proliferation and the sampling distribution from a given shedding episode. We show that while there are distinct differences among the shedding patterns of calves given the same infecting dose, there is no statistically significant difference between the two groups of calves. Such differences as there are, can be explained solely in terms of the shedding frequency, but with all calves potentially excreting the same amount of bacteria in a given shedding episode post-infection. The model can be thought of as a process of the bacteria becoming established in a number of discrete foci of colonization, rather than as a more generalized infection of the respiratory tract. In this case, the variability in the shedding patterns of the infected calves can be explained solely by differences in the number of foci established and shedding being from individual foci over time. Should maximum exposure on a particular occasion be a critical consideration for cattle-to-cattle transmission of BTB, cattle that shed only intermittently may still make an important contribution to the spread and persistence of the disease

KMWin – A Convenient Tool for Graphical Presentation of Results from Kaplan-Meier Survival Time Analysis

BACKGROUND: Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. RESULTS: On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. CONCLUSIONS: We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups