TOPP--the OpenMS proteomics pipeline

MOTIVATION: Experimental techniques in proteomics have seen rapid development over the last few years. Volume and complexity of the data have both been growing at a similar rate. Accordingly, data management and analysis are one of the major challenges in proteomics. Flexible algorithms are required to handle changing experimental setups and to assist in developing and validating new methods. In order to facilitate these studies, it would be desirable to have a flexible 'toolbox' of versatile and user-friendly applications allowing for rapid construction of computational workflows in proteomics. RESULTS: We describe a set of tools for proteomics data analysis-TOPP, The OpenMS Proteomics Pipeline. TOPP provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows. These applications range from useful utilities (file format conversion, peak picking) over wrapper applications for known applications (e.g. Mascot) to completely new algorithmic techniques for data reduction and data analysis. We anticipate that TOPP will greatly facilitate rapid prototyping of proteomics data evaluation pipelines. As such, we describe the basic concepts and the current abilities of TOPP and illustrate these concepts in the context of two example applications: the identification of peptides from a raw dataset through database search and the complex analysis of a standard addition experiment for the absolute quantitation of biomarkers. The latter example demonstrates TOPP's ability to construct flexible analysis pipelines in support of complex experimental setups. AVAILABILITY: The TOPP components are available as open-source software under the lesser GNU public license (LGPL). Source code is available from the project website at www.OpenMS.de     

A statistical approach using network structure in the prediction of protein characteristics

MOTIVATION: The Majority Vote approach has demonstrated that protein-protein interactions can be used to predict the structure or function of a protein. In this article we propose a novel method for the prediction of such protein characteristics based on frequencies of pairwise interactions. In addition, we study a second new approach using the pattern frequencies of triplets of proteins, thus for the first time taking network structure explicitly into account. Both these methods are extended to jointly consider multiple organisms and multiple characteristics. RESULTS: Compared to the standard non-network-based method, namely the Majority Vote method, in large networks our predictions tend to be more accurate. For structure prediction, the Frequency-based method reaches up to 71% accuracy, and the Triplet-based method reaches up to 72% accuracy, whereas for function prediction, both the Triplet-based method and the Frequency-based method reach up to 90% accuracy. Function prediction on proteins without homologues showed slightly less but comparable accuracies. Including partially annotated proteins substantially increases the number of proteins for which our methods predict their characteristics with reasonable accuracy. We find that the enhanced Triplet-based method does not currently yield significantly better results than the enhanced Frequency-based method, suggesting that triplets of interactions do not contain substantially more information about protein characteristics than interaction pairs. Our methods offer two main improvements over current approaches--first, multiple protein characteristics are considered simultaneously, and second, data is integrated from multiple species. In addition, the Triplet-based method includes network structure more explicitly than the Majority Vote and the Frequency-based method. AVAILABILITY: The program is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Resistance to chytridiomycosis varies among amphibian species and is correlated with skin peptide defenses

Innate immune mechanisms of defense are especially important to ectothermic vertebrates in which adaptive immune responses may be slow to develop. One innate defense in amphibian skin is the release of abundant quantities of antimicrobial peptides. Chytridiomycosis is an emerging infectious disease of amphibians caused by the skin fungus, Batrachochytrium dendrobatidis . Susceptibility to chytridiomycosis varies among species, and mechanisms of disease resistance are not well understood. Previously, we have shown that Australian and Panamanian amphibian species that possess skin peptides that effectively inhibit the growth of B. dendrobatidis in vitro tend to survive better in the wild or are predicted to survive the first encounter with this lethal pathogen. For most species, it has been difficult to experimentally infect individuals with B. dendrobatidis and directly evaluate both survival and antimicrobial peptide defenses. Here, we demonstrate differences in susceptibility to chytridiomycosis among four Australian species ( Litoria caerulea, Litoria chloris, Mixophyes fasciolatus and Limnodynastes tasmaniensis ) after experimental infection with B. dendrobatidis , and show that the survival rate increases with the in vitro effectiveness of the skin peptides. We also observed that circulating granulocyte, but not lymphocyte, counts differed between infected and uninfected Lit. chloris . This suggests that innate granulocyte defenses may be activated by pathogen exposure. Taken together, our data suggest that multiple innate defense mechanisms are involved in resistance to chytridiomycosis, and the efficacy of these defenses varies by amphibian species.     

ICOS Mediates the Generation and Function of CD4+CD25+Foxp3+ Regulatory T Cells Conveying Respiratory Tolerance

Costimulatory molecules like ICOS are crucial in mediating T cell differentiation and function after allergen contact and thereby strongly affect the immunologic decision between tolerance or allergy development. In this study, we show in two independent approaches that interruption of the ICOS signaling pathway by application of a blocking anti-ICOSL mAb in wild-type (WT) mice and in ICOS(-/-) mice inhibited respiratory tolerance development leading to eosinophilic airway inflammation, mucus hypersecretion, and Th2 cytokine production in response to OVA sensitization. Respiratory Ag application almost doubled the number of CD4(+)Foxp3(+) regulatory T cells (Tregs) in the lung of WT mice with 77% of lung-derived Tregs expressing ICOS. In contrast, in ICOS(-/-) mice the number of CD4(+)CD25(+)Foxp3(+) Tregs did not increase after respiratory Ag application, and ICOS(-/-) Tregs produced significantly lower amounts of IL-10 than those of WT Tregs. Most importantly, in contrast to WT Tregs, ICOS(-/-) Tregs did not convey protection when transferred to "asthmatic" recipients demonstrating a strongly impaired Treg function in the absence of ICOS signaling. Our findings demonstrate a crucial role of ICOS for the generation and suppressive function of Tregs conveying respiratory tolerance and support the importance of ICOS as a target for primary prevention strategies.     

Relevance of exocytotic glutamate release from retinal glia

Glial cells release molecules that influence brain?development, function, and disease. Calcium-dependent exocytosis has been proposed as potential release mechanism in astroglia, but the physiological relevance of "gliotransmission" in?vivo remains controversial. We focused on the impact of glial exocytosis on sensory transduction in the retina.?To this end, we generated transgenic mice to block exocytosis by Cre recombinase-dependent expression of the clostridial botulinum neurotoxin serotype?B light chain, which cleaves vesicle-associated membrane protein 1-3. Ubiquitous and neuronal toxin expression caused perinatal lethality and?a reduction of synaptic transmission thus validating transgene function. Toxin expression in Müller cells inhibited vesicular glutamate release and impaired glial volume regulation but left retinal histology and visual processing unaffected. Our model to study gliotransmission in?vivo reveals specific functions of exocytotic glutamate release in retinal glia.     

3-Decanol in the haemolymph of the hermit crab Clibanarius vittatus signals shell availability to conspecifics

Hermit crabs with poor fitting shells are chemically attracted to dying gastropods and conspecifics where a shell may become available. For land hermit crabs, the shell cue is a volatile compound found in the haemolymph. Based on this knowledge, we tested the hypothesis that shell investigation behavior in aquatic hermit crabs, the ancestral predecessors of terrestrial hermit crabs, is also triggered by volatile cues. Volatile compounds from haemolymph of Clibanarius vittatus and Pagurus pollicaris and brachyuran decapod crustaceans were purged from a water-haemolymph solution, trapped in seawater and tested for induction of shell investigation behavior with juvenile C. vittatus. Only volatiles from C. vittatus haemolymph stimulated shell investigation. Volatile compounds were isolated from haemolymph by headspace solid-phase microextraction (SPME) and analyzed by coupled gas chromatography-mass spectrometry (GC-MS). Two prominent compounds were identified, 3-decanol, which was unique to C. vittatus haemolymph, and 2-ethyl-1-hexanol, which was present in the haemolymph of all 4 crustacean species. In shell investigation bioassays, 3-decanol from C. vittatus haemolymph stimulated shell investigation behavior, while 2-ethyl-1-hexanol did not. In bioassays with synthetic 1-, 2-, 4-, and 5-decanol, shell investigation behavior was evoked by 1-decanol, 5-decanol and 3-undecanol. There was no response to 2- and 4-decanol. The response of C. vittatus to volatile shell cues supports the hypothesis that volatile cue detection evolved prior to the occupation of terrestrial niches by crustaceans.     

Noninvasive,In Vivo Assessment of Mouse Retinal Structure Using Optical Coherence Tomography

Background

Optical coherence tomography (OCT) is a novel method of retinal in vivo imaging. In this study, we assessed the potential of OCT to yield histology-analogue sections in mouse models of retinal degeneration.

Methodology/Principal Findings

We achieved to adapt a commercial 3^rd generation OCT system to obtain and quantify high-resolution morphological sections of the mouse retina which so far required in vitro histology. OCT and histology were compared in models with developmental defects, light damage, and inherited retinal degenerations. In conditional knockout mice deficient in retinal retinoblastoma protein Rb, the gradient of Cre expression from center to periphery, leading to a gradual reduction of retinal thickness, was clearly visible and well topographically quantifiable. In Nrl knockout mice, the layer involvement in the formation of rosette-like structures was similarly clear as in histology. OCT examination of focal light damage, well demarcated by the autofluorescence pattern, revealed a practically complete loss of photoreceptors with preservation of inner retinal layers, but also more subtle changes like edema formation. In Crb1 knockout mice (a model for Leber''s congenital amaurosis), retinal vessels slipping through the outer nuclear layer towards the retinal pigment epithelium (RPE) due to the lack of adhesion in the subapical region of the photoreceptor inner segments could be well identified.

Conclusions/Significance

We found that with the OCT we were able to detect and analyze a wide range of mouse retinal pathology, and the results compared well to histological sections. In addition, the technique allows to follow individual animals over time, thereby reducing the numbers of study animals needed, and to assess dynamic processes like edema formation. The results clearly indicate that OCT has the potential to revolutionize the future design of respective short- and long-term studies, as well as the preclinical assessment of therapeutic strategies.     

Hygrochastic capsule dehiscence supports safe site strategies in New Zealand alpine Veronica (Plantaginaceae)

Background and Aims

Hygrochasy is a capsule-opening mechanism predominantly associated with plants in arid habitats, where it facilitates spatially and temporally restricted dispersal. Recently, hygrochastic capsules were described in detail for the first time in alpine Veronica in New Zealand. The aim of the present study was to investigate whether hygrochastic capsules are an adaptation of alpine Veronica to achieve directed dispersal to safe sites. We expect that by limiting dispersal to rainfall events, distances travelled by seeds are short and confine them to small habitat patches where both seedlings and adults have a greater chance of survival.

Methods

Dispersal distances of five hygrochastic Veronica were measured under laboratory and field conditions and the seed shadow was analysed. Habitat patch size of hygrochastic Veronica and related non-hygrochastic species were estimated and compared.

Key Results

Dispersal distances achieved by dispersal with raindrops did not exceed 1 m but weather conditions could influence the even distribution of seeds around the parent plant. Compared with related Veronica species, hygrochastic Veronica mostly grow in small, restricted habitat patches surrounded by distinctly different habitats. These habitat patches provide safe sites for seeds due to their microtopography and occurrence of adult cushion plants. Non-hygrochastic Veronica can be predominantly found in large habitats without clearly defined borders and can be spread over long distances along rivers.

Conclusions

The results suggest that hygrochasy is a very effective mechanism of restricting seed dispersal to rainfall events and ensuring short-distance dispersal within a small habitat patch. It appears that it is an adaptation for directed dispersal to safe sites that only exist within the parent habitat.     

Evolution of defences against cuckoo (<Emphasis Type="Italic">Cuculus canorus</Emphasis>) parasitism in bramblings (<Emphasis Type="Italic">Fringilla montifringilla</Emphasis>): a comparison of four populations in Fennoscandia

The brood parasitic common cuckoo Cuculus canorus has a history of coevolution that involves numerous passerine hosts, but today only a subset is known to be regularly parasitised in any area. In some hosts, there is significant variation in the occurrence of parasitism between populations, but still individuals in non-parasitised populations show strong antiparasite defences. In the present study we compared the strength of egg rejection of four distant Fennoscandian brambling Fringilla montifringilla populations experiencing different levels of cuckoo parasitism (0–6%). Egg rejection ability was in general very well developed and we did not find any population differences in the relationship between egg rejection probability and similarity between host and experimental parasitic eggs. Furthermore, bramblings very rarely made errors in rejection, indicating that selection against rejection behaviour is likely to be very weak. The brambling-cuckoo system therefore differs from other well studied systems which are characterised by pronounced spatial and temporal variation in the host’s level of defence. This result is unlikely to reflect independent replication of the same evolutionary trajectory because the weak breeding site tenacity of bramblings should result in an extreme amount of gene flow within the distribution area and thus strongly impede localised responses to selection. Instead, lack of geographic variation has more likely arisen because bramblings respond to selection as one evolutionary unit, and because the average parasitism pressures have been high enough in the past to cause regional fixation of rejection alleles and evolution of clutch characteristics that facilitate cost free egg recognition.