The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model

BACKGROUND

Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics.

RESULTS

Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm's natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode's transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm's defense against fungal pathogens in vivo.

CONCLUSION

This first systematic analysis of the nematode's native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm's biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a tractable model for the in-depth dissection of host-microbiome interactions.

Liver fibrosis during the development of biliary atresia: Proof of principle in the murine model

BACKGROUND

The murine model of biliary atresia (BA) is used for examining the pathogenesis of BA. The aim of the study was description of the morphological features and illustrating the detailed development of fibrosis using the Biliary Atresia Research Consortium (BARC) system.

METHODS

Neonatal mice were injected intraperitoneally with rhesus rotavirus (RRV) strain (N=17). Healthy mice were the control group (N=29). All mice were sacrificed at 7 or 14days after birth. Two pathologists examined the morphological features using the BARC system; CK19, αSMA and collagen type I were assessed by immunohistochemistry.

RESULTS

In RRV mice, portal fibrous expansion with focal bile duct proliferation and strong portal cellular infiltrate was found in contrast to healthy mice. In RRV mice, CK19 bile duct staining was significantly less or absent (p<0.01), with stronger portal staining of collagen type I (p=0.02). Expansion of staining for αSMA was more in RRV mice (p<0.01), but αSMA portal staining was stronger in healthy mice (p=0.02).

CONCLUSIONS

The morphological features observed in the murine model of BA correspond with the BA characteristics according to the BARC criteria. Fibrosis is an important feature of the model. Therefore, this murine model is useful for investigating the pathogenesis of BA.

Ten years of life in compost: temporal and spatial variation of North German Caenorhabditis elegans populations

The nematode Caenorhabditis elegans is a central laboratory model system in almost all biological disciplines, yet its natural life history and population biology are largely unexplored. Such information is essential for in-depth understanding of the nematode's biology because its natural ecology provides the context, in which its traits and the underlying molecular mechanisms evolved. We characterized natural phenotypic and genetic variation among North German C. elegans isolates. We used the unique opportunity to compare samples collected 10 years apart from the same compost heap and additionally included recent samples for this and a second site, collected across a 1.5-year period. Our analysis revealed significant population genetic differentiation between locations, across the 10-year time period, but for only one location a trend across the shorter time frame. Significant variation was similarly found for phenotypic traits of likely importance in nature, such as choice behavior and population growth in the presence of pathogens or naturally associated bacteria. Phenotypic variation was significantly influenced by C. elegans genotype, time of isolation, and sampling site. The here studied C. elegans isolates may provide a valuable, genetically variable resource for future dissection of naturally relevant gene functions.

Travelling at a slug's pace: possible invertebrate vectors of Caenorhabditis nematodes

Background

How do very small animals with limited long-distance dispersal abilities move between locations, especially if they prefer ephemeral micro-habitats that are only available for short periods of time? The free-living model nematode Caenorhabditis elegans and several congeneric taxa appear to be common in such short-lived environments, for example decomposing fruits or other rotting plant material. Dispersal is usually assumed to depend on animal vectors, yet all current data is based on only a limited number of studies. In our project we performed three comprehensive field surveys on possible invertebrate vectors in North German locations containing populations of C. elegans and two related species, especially C. remanei, and combined these screens with an experimental analysis of persistence in one of the vector taxa.

Results

Our field survey revealed that Caenorhabditis nematodes are commonly found in slugs, isopods, and chilopods, but are not present in the remaining taxonomic groups examined. Surprisingly, the nematodes were frequently isolated from the intestines of slugs, even if slugs were not collected in close association with suitable substrates for Caenorhabditis proliferation. This suggests that the nematodes are able to enter the slug intestines and persist for certain periods of time. Our experimental analysis confirmed the ability of C. elegans to invade slug intestines and subsequently be excreted alive with the slug feces, although only for short time periods under laboratory conditions.

Conclusions

We conclude that three invertebrate taxonomic groups represent potential vectors of Caenorhabditis nematodes. The nematodes appear to have evolved specific adaptations to enter and persist in the harsh environment of slug intestines, possibly indicating first steps towards a parasitic life-style.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-015-0050-z) contains supplementary material, which is available to authorized users.

Tomographic imaging of nonsymmetric multicomponent tailored supersonic flows from structured gas nozzles

We report experimental results on the production and characterization of asymmetric and composite supersonic gas flows, created by merging independently controllable flows from multiple nozzles. We demonstrate that the spatial profiles are adjustable over a large range of parameters, including gas density, density gradient, and atomic composition. The profiles were precisely characterized using three-dimensional tomography. The creation and measurement of complex gas flows is relevant to numerous applications, ranging from laser-produced plasmas to rocket thrusters.

Regional radiotherapy in high-risk breast cancer: is the issue solved?

Adjuvant radiotherapy is the treatment standard for breast cancer with lymph node metastases after breast-conserving surgery or mastectomy. The inclusion of regional lymph nodes into the treatment volumes has been a question in recent clinical trials. Their impact on treatment standards and open questions is discussed.

Involvement of ATM in homologous recombination after end resection and RAD51 nucleofilament formation

Ataxia-telangiectasia mutated (ATM) is needed for the initiation of the double-strand break (DSB) repair by homologous recombination (HR). ATM triggers DSB end resection by stimulating the nucleolytic activity of CtIP and MRE11 to generate 3′-ssDNA overhangs, followed by RPA loading and RAD51 nucleofilament formation. Here we show for the first time that ATM is also needed for later steps in HR after RAD51 nucleofilament formation. Inhibition of ATM after completion of end resection did not affect RAD51 nucleofilament formation, but resulted in HR deficiency as evidenced by (i) an increase in the number of residual RAD51/γH2AX foci in both S and G2 cells, (ii) the decrease in HR efficiency as detected by HR repair substrate (pGC), (iii) a reduced SCE rate and (iv) the radiosensitization of cells by PARP inhibition. This newly described role for ATM was found to be dispensable in heterochromatin-associated DSB repair, as KAP1-depletion did not alleviate the HR-deficiency when ATM was inhibited after end resection. Moreover, we demonstrated that ATR can partly compensate for the deficiency in early, but not in later, steps of HR upon ATM inhibition. Taken together, we describe here for the first time that ATM is needed not only for the initiation but also for the completion of HR.

Legal and regulatory considerations associated with use of patient-generated health data from social media and mobile health (mHealth) devices

Patient-generated health data are coming into broader use across the health care spectrum and hold great promise as a means to improve care and health outcomes. At the same time, rapid evolution in the social media and mobile health (mHealth) market has promoted an environment in which creation and transmission of personal health information is easy, quick, and appealing to patients. However, adoption of social media and mHealth by providers is hampered by legal and regulatory concerns with regard to data ownership and data use. This article defines common forms of patient-generated health data (PGHD) and describes how PGHD is used in clinical settings. It explores issues related to protection of personal health information, including that of children and adolescents, data security, and other potential barriers such as physician licensure. It also discusses regulatory and legal considerations providers and patients should consider before using social media and mobile health apps.

Why we need more ecology for genetic models such as C. elegans

Functional information about the large majority of the genes is still lacking in the classical eukaryotic model species Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus. Because many of these genes are likely to be important in natural settings, considering explicit ecological information should increase our knowledge of gene function. Using C. elegans as an example, we discuss the importance of biotic factors as a driving force in shaping the composition and structure of the nematode genome. We highlight examples for which consideration of ecological information and natural variation have been key to the identification of novel, unexpected gene functions, and use these examples to define future research avenues for the classical genetic model taxa.

Modifications in integrin expression and extracellular matrix composition in children with biliary atresia

BACKGROUND

The aetiology of biliary atresia (BA) is still unresolved. The study's aim was to investigate the distribution of extracellular matrix proteins and cellular adhesion molecules in children with BA compared to other cholestatic liver disease (CLD) and normal liver architecture (NLA).

PATIENTS

Liver biopsies were obtained from children with BA (n=13), CLD (n=6) and NLA (n=8).

METHOD

We systematically analysed ultra thin frozen sections from the liver hilum stained with 25 monoclonal antibodies for cellular characterisation, extracellular matrix proteins and adhesion molecules.

RESULTS

2 changes were specifically found in BA: laminin beta1 was reduced in children with BA vs. NLA and CLD. Conversely, integrin alpha 3 was increased in BA vs. NLA and CLD (p<0.05). Furthermore, we detected changes in a similar pattern for both BA and CLD vs. NLA: in BA and CLD perlecan was increased. On the contrary, integrin beta1 and entactin were decreased vs. NLA (p<0.05).

DISCUSSION

Extracellular matrix proteins and adhesion molecules mediate cellular polarity and integrity, development of tubular structures, and proliferation. Therefore, our findings can be important for the understanding of the genesis of BA.

CONCLUSION

The composition of extracellular matrix proteins and adhesion molecules in children with BA differs from NLA and other CLD in distribution of laminin beta1 and integrin alpha 3, which may have implications for genetic, immunologic and environmental associations in BA.

Canadian Drug Regulatory Framework

The role of regulatory drug submission evaluators in Canada is to critically assess both the data submitted and the sponsor's interpretation of the data in order to reach an evidence-, and context- based recommendation as to the potential benefits and potential harms (i.e., risks) associated with taking the drug under the proposed conditions of use. The purpose of this document is to outline the regulatory framework in which this assessment occurs, including: defining what “authorization to market a drug in Canada” means, in terms of the role of the sponsor, the responsibility of Health Canada in applying the Food and Drugs Act prior to and after marketing authorization, and the distinction between regulatory authorization versus physician authorization; highlighting organizational, process and legal factors within Health Canada related to authorization of clinical trials and authorization to market a drug; considerations during the review process, such as regulatory and scientific issues related to the drug, patient populations and trial designs; application of international guidelines, and decisions from other jurisdictions; regulatory realities regarding drug authorization, including the requirement for wording in the Product Monograph to accurately reflect the information currently available on the safe and effective use of a drug, and that hypothesis-confirming studies are essential to regulatory endorsement; current issues related to the review of therapies for dementia, such as assessing preventative treatments, and therapies that have symptomatic versus disease-modifying effects, statistical issues regarding missing data, and trial design issues.

Right ventricular stroke volume variation: a tool to assess right ventricular volume responsiveness

BACKGROUND

So far, only left ventricular functional preload indices are used as a routine to assess volume responsiveness. Right ventricular (RV) functional preload indices have been described, but offer no continuous monitoring.

METHODS

Following ethical approval, a pressure-induced right ventricular failure (RVF) was induced with continuous infusion of a thromboxane-A2-analogue (U46619) in 15 anesthetized and ventilated pigs. Before and after increasing mean pulmonary artery pressure (MPAP) by 50%, right ventricular stroke volume variation (RVSVV) was assessed with an ultrasonic pulmonary artery flow probe. Measurements were repeated following volume depletion (- 300 mL) and stepwise retransfusion (200 mL of whole blood and 200 mL of a colloid solution).

RESULTS

A significant and systematic increase in RVSVV during induction of RVF was observed. Volume depletion led to an increase in RVSVV and re-transfusion led to a decrease in RVSVV. RVSVV was higher and a significant decrease in RVSVV was present in all animals experiencing an increase in CO by more than 5% during retransfusion.

CONCLUSION

RVSVV seems to reflect volume requirement of the right ventricle and it might prove a reliable parameter to assess volume responsiveness in RVF.

Big Data in Healthcare - Defining the Digital Persona through User Contexts from the Micro to the Macro. Contribution of the IMIA Organizational and Social Issues WG

OBJECTIVES

While big data offers enormous potential for improving healthcare delivery, many of the existing claims concerning big data in healthcare are based on anecdotal reports and theoretical vision papers, rather than scientific evidence based on empirical research. Historically, the implementation of health information technology has resulted in unintended consequences at the individual, organizational and social levels, but these unintended consequences of collecting data have remained unaddressed in the literature on big data. The objective of this paper is to provide insights into big data from the perspective of people, social and organizational considerations.

METHOD

We draw upon the concept of persona to define the digital persona as the intersection of data, tasks and context for different user groups. We then describe how the digital persona can serve as a framework to understanding sociotechnical considerations of big data implementation. We then discuss the digital persona in the context of micro, meso and macro user groups across the 3 Vs of big data.

RESULTS

We provide insights into the potential benefits and challenges of applying big data approaches to healthcare as well as how to position these approaches to achieve health system objectives such as patient safety or patient-engaged care delivery. We also provide a framework for defining the digital persona at a micro, meso and macro level to help understand the user contexts of big data solutions.

CONCLUSION

While big data provides great potential for improving healthcare delivery, it is essential that we consider the individual, social and organizational contexts of data use when implementing big data solutions.

The prevalence of Caenorhabditis elegans across 1.5 years in selected North German locations: the importance of substrate type, abiotic parameters, and Caenorhabditis competitors

BACKGROUND

Although the nematode Caenorhabditis elegans is a major model organism in diverse biological areas and well studied under laboratory conditions, little is known about its ecology. Therefore, characterization of the species' natural habitats should provide a new perspective on its otherwise well-studied biology. The currently best characterized populations are in France, demonstrating that C. elegans prefers nutrient- and microorganism-rich substrates such as rotting fruits and decomposing plant matter. In order to extend these findings, we sampled C. elegans continuously across 1.5 years from rotting apples and compost heaps in three North German locations.

RESULTS

C. elegans was found throughout summer and autumn in both years. It shares its habitat with the related nematode species C. remanei, which could thus represent an important competitor for a similar ecological niche. The two species were isolated from the same site, but rarely the same substrate sample. In fact, C. elegans was mainly found on compost and C. remanei on rotten apples, possibly suggesting niche separation. The occurrence of C. elegans itself was related to environmental humidity and rain, although the correlation was significant for only one sampling site each. Additional associations between nematode prevalence and abiotic parameters could not be established.

CONCLUSIONS

Taken together, our findings vary from the previous results for French C. elegans populations in that the considered German populations always coexisted with the congeneric species C. remanei (rather than C. briggsae as in France) and that C. elegans prevalence can associate with humidity and rain (rather than temperature, as suggested for French populations). Consideration of additional locations and time points is thus essential for full appreciation of the nematode's natural ecology.