ESCMID postgraduate technical workshop on intracellular bacteria: from biology to clinic.

Infection by intracellular bacteria can lead to several diseases in both veterinary and human medicine. Unfortunately, the biology of these intracellular bacteria is highly complex due to their interactions with their host cells. Thus, it is very important to develop several tools in order to better understand the complex intracellular life of these pathogens, so allowing to improve the diagnosis options and the treatments of infectious diseases that they are causing. The workshop organised in Villars-sur-Ollon (Switzerland) by the ESCMID Study group on intracellular bacteria was a good opportunity to enhance our knowledge on these fastidious pathogens. During 5 days, 15 speakers gave 41 talks, covering all fields, from biology to clinic of different intracellular bacteria such as Bartonella, Chlamydia, Coxiella, Ehrlichia, Listeria, Parachlamydia, Rickettsia, and Waddlia. The format of this postgraduate course, which took place in the Swiss mountains, allowed interactive sessions and living discussions between the participants coming from all around the world. One of the major strength was to gather epidemiologists, clinical microbiologists, infectious diseases specialists, entomologists, veterinarians as well as bioinformaticians, biochemists and biologists to deliver a unique "one-health science" on intracellular bacteria. Here, we summarise the main take-home messages delivered during this meeting.

Hémato-oncologie pédiatrique: de la biologie cellulaire aux traitements ciblés et individualisés [Pediatric hemato-oncology: from cellular biology to individualized targeted therapies].

Progresses in pediatric oncology over the last decades have been dramatic and allow current cure rates above 80%. There are mainly due to multicentre clinical trials aiming at optimizing chemotherapy protocols as well as local therapies in a stepwise approach. Most of the new anticancer drugs currently in development are based on targeted therapies, directed to specific targets present only in or on tumor cells, like growth factor receptors, mechanisms involved in proliferation, DNA repair, apoptosis, tumor invasion or angiogenesis. Concerning bone marrow transplantation also, new strategic approaches are in advanced development. They aim at reducing treatment induced toxicity and enhancing efficacy at the same time. This short paper would like to point out these new technologies, which should be known by the general practitioner.

Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

Genome Biology and Evolution of the Animal Kingdom

Estudi realitzat a partir d’una estada a la Institut J.W. Jenkinson Laboratory for Evolution and Development of the University of Oxford, Regne Unit, entre 2010 i 2012. He estat membre del laboratori del Professor Peter W.H. Holland com a becari post-doctoral Beatriu de Pinós des de setembre de 2010 al setembre de 2012. El nostre projecte de recerca se centra en l'anàlisi genòmic comparatiu del Regne Animal, tot explorant el contingut dels genomes a través de totes les branques de l'arbre dels animals. Totes les referències a les meves publicacions durant aquest post-doc es poden trobar a http://about.me/jordi_paps. Crec que el nombre i la qualitat dels resultats del meu post-doc, un total de 8 publicacions incloent dos articles a la prestigiosa revista Nature, són prova de l'èxit d'aquest post-doc. Prof Peter W. H. Holland (Departament de Zoologia de la Universitat d'Oxford) i jo som coautors de tres articles de genòmica comparativa, resultats directes d'aquest projecte: 1) comparació de families gèniques entre vertebrats invertebrats (Briefings in Functional Genomics), 2) el genoma de l'ostra (publicat a la revista Nature), i 3) els genomes de 6 platihelmints paràsits (acceptat també a Nature). A més, tenim altres 2 treballs en preparació. Un d'ells analitza l'evolució, expressió i funció dels gens Hox al a la tènia Hymenolepis. El perfil fi d'aquests gens clau del desenvolupament esclareix els canvis d'estil de vida dels organismes. A més, durant aquest últim post-doc he participat en diverses col•laboracions, incloent anàlisi de gens d'envelliment a cucs plans, un estudi sobre la filogènia del grup Gastrotricha, una revisió de l'evolució phylum Platyhelminthes, així com un capítol d'un llibre sobre l'evolució dels animals bilaterals. Finalment, gràcies a la beca Beatriu de Pinós, el Prof. Peter W.H. Holland m'ha convidat a formar part del seu equip com un investigador post-doctoral en el seu projecte ERC Advance actual sobre duplicacions genòmiques.

FIB-SEM tomography in biology.

Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

HER2 shedding and serum HER2 extracellular domain: Biology and clinical utility in breast cancer.

The transmembrane protein HER2 is over-expressed in approximately 15% of invasive breast cancers as a result of HER2 gene amplification. HER2 proteolytic cleavage (HER2 shedding) generates soluble truncated HER2 molecules that include only the extracellular domain and the concentration of which can be measured in the serum fraction of blood. HER2 shedding also generates a constitutively active truncated intracellular receptor of 95kDa (p95(HER2)). Another soluble truncated HER2 protein (Herstatin), which can also be found in serum, is the product of an alternatively spliced HER2 transcript. Recent preclinical findings may provide crucial insights into the biological and clinical relevance of increased sHER2 concentrations for the outcome of HER2-positive breast cancer and sensitivity to trastuzumab and lapatinib treatment. We present here the most recent findings about the role and biology of sHER2 based on data obtained using a standardized test, which has been cleared by FDA in 2000, for measuring sHER2. This test includes quality control assessments and has been already widely used to evaluate the clinical utility of sHER2 as a biomarker in breast cancer. We will describe in detail data concerning the assessment of sHER2 as a surrogate maker to optimize the evaluation of the HER2 status of a primary tumor and as a prognosis and predictive marker of response to therapies, both in early and metastatic breast cancer.

Can fisheries-induced evolution shift reference points for fisheries management?

Biological reference points are important tools for fisheries management. Reference points are not static, but may change when a population's environment or the population itself changes. Fisheries-induced evolution is one mechanism that can alter population characteristics, leading to "shifting" reference points by modifying the underlying biological processes or by changing the perception of a fishery system. The former causes changes in "true" reference points, whereas the latter is caused by changes in the yardsticks used to quantify a system's status. Unaccounted shifts of either kind imply that reference points gradually lose their intended meaning. This can lead to increased precaution, which is safe, but potentially costly. Shifts can also occur in more perilous directions, such that actual risks are greater than anticipated. Our qualitative analysis suggests that all commonly used reference points are susceptible to shifting through fisheries-induced evolution, including the limit and "precautionary" reference points for spawning-stock biomass, Blim and Bpa, and the target reference point for fishing mortality, F0.1. Our findings call for increased awareness of fisheries-induced changes and highlight the value of always basing reference points on adequately updated information, to capture all changes in the biological processes that drive fish population dynamics.

Type of prey influences biology and consumption rate of Orius insidiosus (Say) (Hemiptera, Anthocoridae)

Generalist predators are capable of consuming different types of prey, and as each prey may have distinct nutritional values, each may have a distinct impact on the biology of the predator. Therefore, the aim of this study was to determine how the consumption of different prey influences certain biological characteristics and the predatory capacity of Orius insidiosus (Say). The investigation was performed in climatic chamber at 25 ±1 ºC, RH 70 ± 10% and fotophase 12. Eggs of Anagasta kuehniella (Zeller), adults of Caliothrips phaseoli (Hood) and nymphs of Aphis gossypii Glover were used as prey and were provided daily ad libitum for all the mobile stages of the predator. The results showed that biological parameters of O. insidiosus are affected differently depending on the type of prey ingested. The development time of the nymphal stage was 13.1, 11.23 and 10.25 days for O. insidiosus feeding on eggs of A. kuehniella, nymphs of A. gossypii and adults of C. phaseoli, respectively. Longevity was five times larger for adults fed on eggs of A. kuehniella (56.25 days) compared to that of adults that preyed on nymphs of A. gossypii (11.44 days), and four times larger when the prey were adults of C. phaseoli (13.58 days). The consumption of eggs of A. kuehniella by predator females resulted in a shorter pre-oviposition period (3.2 days) and a longer oviposition period (44.4 days) when compared to the consumption of other types of prey. In addition, fecundity was increased with the consumption of eggs of A. kuehniella (195.25 eggs laid / female) when compared to feeding on the other prey, C. phaseoli (70.00 eggs laid / female) or A. gossypii (22.50 eggs laid / female). However, the consumption of aphids was larger (148.28 nymphs/ nymphal stage) than that of thrips (74.10 thrips / nymphal stage) or eggs of A. kuehniella (37.03 eggs /nymphal stage) for all of the nymphal stages of the predator. The results indicate that the eggs of A. kuehniella are the type of prey best suited for rearing this predator insect under laboratory conditions. Also fecundity was better with this prey even though the predator consumed during its nymphal stage a lesser quantity of eggs compared to the other prey.

Comparative biology of Cycloneda sanguinea (Linnaeus, 1763) and Hippodamia convergens Guérin-Méneville, 1842 (Coleoptera, Coccinellidae) focusing on the control of Cinara spp. (Hemiptera, Aphididae)

The giant conifer aphids Cinara pinivora (Wilson, 1919) and Cinara atlantica (Wilson, 1919) (Hemiptera, Aphididae) have been observed attacking Pinus spp. in Southern and Southeastern Brazil. The coccinellids, on the other hand, were found feeding on these aphids in the field, which can be regarded as potential biological control agents. The biological cycle and mortality rate of larvae of Cycloneda sanguinea (Linnaeus, 1763) and Hippodamia convergens Guérin-Méneville, 1842 (Coleoptera, Coccinellidae) were evaluated using twenty larvae of each predator species fed with nymphs of Cinara. The vials with the insects were kept under 15 ºC, 20 ºC and 25 ºC, with 12h photophase and 70 ± 10% relative humidity. The consumption was evaluated every 24 hours and the nymphs replaced. For C. sanguinea, the egg incubation time was 10.5, 5.0 and 4.0 days; the average larval development period was 33.3, 15.8 and 8.6 days and the larval mortality rate 20%,0% and 15%, respectively at 15 ºC, 20 ºC and 25 ºC. For H. convergens, the larval development time was 41.9, 19.3 and 10.9 days at 15 ºC, 20 ºC and 25 ºC, respectively. The larval mortality rate was 35%, 15% and 0% under the three temperatures. Both species developed adequately when fed nymphs of Cinara, however, C. sanguinea performed better than H. convergens, even at 15 ºC, at which temperature the biological cycles of the coccinellids are prolonged, but the temperature is favorable for the development of Cinara populations in the field.

Floral biology of Stachytarpheta maximiliani Scham. (Verbenaceae) and its floral visitors

This study describes the reproductive system of Stachytarpheta maximiliani (Verbenaceae), including its floral biology, nectar and pollen availability and insect foraging patterns, identifying whose species act as pollinators. It was carried out in a Brazilian Atlantic rain forest site. Observations on the pollination biology of the Verbenaceae S. maximiliani indicate that their flowering period extends from September through May. Anthesis occurs from 5:30 a.m. to 5:00 p.m. and nectar and pollen are available during all the anthesis. Many species of beetles, hemipterans, flies, wasps, bees and butterflies visit their flowers, but bees and butterflies are the most frequent visitors. The flowers are generally small, gathered in dense showy inflorescences. A complex of floral characteristcs, such as violet-blue color of flowers, long floral tubes, without scents, nectar not exposed, high concentration of sugar in nectar (about 32%), allowed identification of floral syndromes (melittophily and psicophily) and function for each visitor. The bees, Bombus morio, B. atratus, Trigonopedia ferruginea, Xylocopa brasilianorum and Apis mellifera and the butterflies Corticea mendica mendica, Corticea sp., Vehilius clavicula, Urbanus simplicius, U. teleus and Heraclides thoas brasiliensis, are the most important pollinators.

Nesting biology of the trap-nesting Neotropical wasp Trypoxylo n(Trypargilum) aurifrons Shuckard (Hymenoptera, Crabronidae)

The present study was carried out in three localities of the state of São Paulo, Brazil: Araras (Dec/03-Dec/06), São Carlos (Nov/04-Nov/06) and Rifaina (Jul/04-Dec/06). Trap-nests were distributed among sites in the sampling areas and were collected every 35 days. Data from 295 nests indicate that T. aurifrons is a multivoltine species, with higher rates of nest building and cell production in the warm, rainy season. The trap-nests used by the females ranged from 117 to 467 mm in length and 3.1 to 16.6 mm in diameter. All nests showed deep plugs and a vestibular cell was found in 37% of the complete nests. The number of cells per nest ranged from one to 12. Females were larger than males, emerged from longer cells and their cocoons were significantly larger. A secondary 1:1 sex ratio was found in Araras and Rifaina. No correlation was observed between the diameter of the trap-nest and sex ratio. Males were usually oviposited in the first brood cells. Male and female developmental time from egg to adult was longer in the cold, dry season. Trypoxylon aurifrons provisioned their nests mainly with orb-spiders from the family Araneidae. The most important mortality factor was the death of immature forms, probably due to development failure. The most important parasitoid was Melittobia sp.