Data management and data analysis in the large European projects GEHA (GEnetics of Healthy Aging) and NU-AGE (NUtrition and AGEing): a bioinformatic approach

The aging process is characterized by the progressive fitness decline experienced at all the levels of physiological organization, from single molecules up to the whole organism. Studies confirmed inflammaging, a chronic low-level inflammation, as a deeply intertwined partner of the aging process, which may provide the “common soil” upon which age-related diseases develop and flourish. Thus, albeit inflammation per se represents a physiological process, it can rapidly become detrimental if it goes out of control causing an excess of local and systemic inflammatory response, a striking risk factor for the elderly population. Developing interventions to counteract the establishment of this state is thus a top priority. Diet, among other factors, represents a good candidate to regulate inflammation. Building on top of this consideration, the EU project NU-AGE is now trying to assess if a Mediterranean diet, fortified for the elderly population needs, may help in modulating inflammaging. To do so, NU-AGE enrolled a total of 1250 subjects, half of which followed a 1-year long diet, and characterized them by mean of the most advanced –omics and non –omics analyses. The aim of this thesis was the development of a solid data management pipeline able to efficiently cope with the results of these assays, which are now flowing inside a centralized database, ready to be used to test the most disparate scientific hypotheses. At the same time, the work hereby described encompasses the data analysis of the GEHA project, which was focused on identifying the genetic determinants of longevity, with a particular focus on developing and applying a method for detecting epistatic interactions in human mtDNA. Eventually, in an effort to propel the adoption of NGS technologies in everyday pipeline, we developed a NGS variant calling pipeline devoted to solve all the sequencing-related issues of the mtDNA.

The role of bifidobacteria in newborn health and the intestinal microbial balance

Gut microbial acquisition during the early stage of life is an extremely important event since it affects the health status of the host. In this contest the healthy properties of the genus Bifidobacterium have a central function in newborns. The aim of this thesis was to explore the dynamics of the gut microbial colonization in newborns and to suggest possible strategies to maintain or restore a correct balance of gut bacterial population in infants. The first step of this work was to review the most recent studies on the use of probiotics and prebiotics in infants. Secondly, in order to prevent or treat intestinal disorders that may affect newborns, the capability of selected Bifidobacterium strains to reduce the amount of Enterobacteriaceae and against the infant pathogen Streptococcus agalactiae was evaluated in vitro. Furthermore, the ability of several commercial fibers to stimulate selectively the growth of bifidobacterial strains was checked. Finally, the gut microbial composition in the early stage of life in response to the intrapartum antibiotic prophylaxis (IAP) against group B Streptococcus was studied using q-PCR, DGGE and next generation sequencing. The results globally showed that Bifidobacterium breve B632 strain is the best candidate for the use in a synbiotic product coupled to a mixture of two selected prebiotic fibers (galactooligosaccharides and fructooligosaccharides) for gastrointestinal disorders in infants. Moreover, the early gut microbial composition was affected by IAP treatment with infants showing lower counts of Bifidobacterium spp. and Bacteroides spp. coupled to a decrement of biodiversity of bacteria, compared to control infants. These studies have shown that IAP could affect the early intestinal balance in infants and they have paved the way to the definition of new strategies alternative to antibiotic treatment to control GBS infection in pregnant women.

Microbial ecology of biotechnological processes

The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

Bioremediation of PCB-contaminated marine sediments: From identification of indigenous dehalorespirers to enhancement of microbial reductive dechlorination

Marine sediments are the main accumulation reservoir of organic recalcitrant pollutants such as polychlorinated biphenyls (PCBs). In the anoxic conditions typical of these sediments, anaerobic bacteria of the phylum Chloroflexi are able to attack these compounds in a process called microbial reductive dechlorination. Such activity and members of this phylum were detected in PCB-impacted sediments of the Venice Lagoon. The aim of this work was to investigate microbial reductive dechlorination and design bioremediation approaches for marine sediments of the area. Three out of six sediment cultures from different sampling areas exhibited dechlorination activities in the same conditions of the site and two phylotypes (VLD-1 and VLD-2) were detected and correlated to this metabolism. Biostimulation was tested on enriched dechlorinating sediment cultures from the same site using five different electron donors, of which lactate was the best biostimulating agent; complementation of microbial and chemical dechlorination catalyzed by biogenic zerovalent Pd nanoparticles was not effective due to sulfide poisoning of the catalyst. A new biosurfactant-producing strain of Shewanella frigidimarina was concomitantly obtained from hydrocarbon-degrading marine cultures and selected because of the low toxicity of its product. All these findings were then exploited to develop bioremediation lab-scale tests in shaken reactors and static microcosms on real sediments and water of the Venice lagoon, testing i) a bioaugmentation approach, with a selected enriched sediment culture from the same area, ii) a biostimulation approach with lactate as electron donor, iii) a bioavailability enhancement with the supplementation of the newly-discovered biosurfactant, and iv) all possible combinations of the afore-mentioned approaches. The best bioremediation approach resulted to be a combination of bioaugmentation and bioremediation and it could be a starting point to design bioremediation process for actual marine sediments of the Venice Lagoon area.

Microfluidic microbial fuel cell fabrication and rapid screening of electrochemically microbes

The demand for novel renewable energy sources, together with the new findings on bacterial electron transport mechanisms and the progress in microbial fuel cell design, have raised a noticeable interest in microbial power generation. Microbial fuel cell (MFC) is an electrochemical device that converts organic substrates into electricity via catalytic conversion by microorganism. It has represented a continuously growing research field during the past few years. The great advantage of this device is the direct conversion of the substrate into electricity and in the future, MFC may be linked to municipal waste streams or sources of agricultural and animal waste, providing a sustainable system for waste treatment and energy production. However, these novel green technologies have not yet been used for practical applications due to their low power outputs and challenges associated with scale-up, so in-depth studies are highly necessary to significantly improve and optimize the device working conditions. For the time being, the micro-scale MFCs show great potential in the rapid screening of electrochemically active microbes. This thesis presents how it will be possible to optimize the properties and design of the micro-size microbial fuel cell for maximum efficiency by understanding the MFC system. So it will involve designing, building and testing a miniature microbial fuel cell using a new species of microorganisms that promises high efficiency and long lifetime. The new device offer unique advantages of fast start-up, high sensitivity and superior microfluidic control over the measured microenvironment, which makes them good candidates for rapid screening of electrode materials, bacterial strains and growth media. It will be made in the Centre of Hybrid Biodevices (Faculty of Physical Sciences and Engineering, University of Southampton) from polymer materials like PDMS. The eventual aim is to develop a system with the optimum combination of microorganism, ion exchange membrane and growth medium. After fabricating the cell, different bacteria and plankton species will be grown in the device and the microbial fuel cell characterized for open circuit voltage and power. It will also use photo-sensitive organisms and characterize the power produced by the device in response to optical illumination.

Atmospheric plasma processes for microbial inactivation: food applications and stress response in Listeria monocytogenes

This PhD thesis is focused on cold atmospheric plasma treatments (GP) for microbial inactivation in food applications. In fact GP represents a promising emerging technology alternative to the traditional methods for the decontamination of foods. The objectives of this work were to evaluate: - the effects of GP treatments on microbial inactivation in model systems and in real foods; - the stress response in L. monocytogenes following exposure to different GP treatments. As far as the first aspect, inactivation curves were obtained for some target pathogens, i.e. Listeria monocytogenes and Escherichia coli, by exposing microbial cells to GP generated with two different DBD equipments and processing conditions (exposure time, material of the electrodes). Concerning food applications, the effects of different GP treatments on the inactivation of natural microflora and Listeria monocytogenes, Salmonella Enteritidis and Escherichia coli on the surface of Fuji apples, soya sprouts and black pepper were evaluated. In particular the efficacy of the exposure to gas plasma was assessed immediately after treatments and during storage. Moreover, also possible changes in quality parameters such as colour, pH, Aw, moisture content, oxidation, polyphenol-oxidase activity, antioxidant activity were investigated. Since the lack of knowledge of cell targets of GP may limit its application, the possible mechanism of action of GP was studied against 2 strains of Listeria monocytogenes by evaluating modifications in the fatty acids of the cytoplasmic membrane (through GC/MS analysis) and metabolites detected by SPME-GC/MS and 1H-NMR analyses. Moreover, changes induced by different treatments on the expression of selected genes related to general stress response, virulence or to the metabolism were detected with Reverse Transcription-qPCR. In collaboration with the Scripps Research Institute (La Jolla, CA, USA) also proteomic profiles following gas plasma exposure were analysed through Multidimensional Protein Identification Technology (MudPIT) to evaluate possible changes in metabolic processes.

Impact of anthropogenic stressors on the population genetics of the common bioindicator Dreissena polymorpha (Pallas, 1771)

Toxicant inputs from agriculture, industry and human settlements have been shown to severely affect freshwater ecosystems. Pollution can lead to changes in population genetic patterns through various genetic and stochastic processes. In my thesis, I investigated the impact of anthropogenic stressors on the population genetics of the zebra mussel Dreissena polymorpha. In order to analyze the genetics of zebra mussel populations, I isolated five new highly polymorphic microsatellite loci. Out of those and other already existing microsatellite markers for this species, I established a robust marker set of six microsatellite loci for D. polymorpha. rnMonitoring the biogeographical background is an important requirement when integrating population genetic measures into ecotoxicological studies. I analyzed the biogeographical background of eleven populations in a section of the River Danube (in Hungary and Croatia) and some of its tributaries, and another population in the River Rhine as genetic outgroup. Moreover, I measured abiotic water parameters at the sampling sites and analyzed if they were correlated with the genetic parameters of the populations. The genetic differentiation was basically consistent with the overall biogeographical history of the populations in the study region. However, the genetic diversity of the populations was not influenced by the geographical distance between the populations, but by the environmental factors oxygen and temperature and also by other unidentified factors. I found strong evidence that genetic adaptation of zebra mussel populations to local habitat conditions had influenced the genetic constitution of the populations. Moreover, by establishing the biogeographical baseline of molecular variance in the study area, I laid the foundation for interpreting population genetic results in ecotoxicological experiments in this region.rnIn a cooperation project with the Department of Zoology of the University of Zagreb, I elaborated an integrated approach in biomonitoring with D. polymorpha by combining the analysis techniques of microsatellite analysis, Comet assay and micronucleus test (MNT). This approach was applied in a case study on freshwater contamination by an effluent of a wastewater treatment plant (WWTP) in the River Drava (Croatia) and a complementary laboratory experiment. I assessed and compared the genetic status of two zebra mussel populations from a contaminated and a reference site. Microsatellite analysis suggested that the contaminated population had undergone a genetic bottleneck, caused by random genetic drift and selection, whereas a bottleneck was not detected in the reference population. The Comet assay did not indicate any difference in DNA damage between the two populations, but MNT revealed that the contaminated population had an increased percentage of micronuclei in hemocytes in comparison to the reference population. The laboratory experiment with mussels exposed to municipal wastewater revealed that mussels from the contaminated site had a lower percentage of tail DNA and a higher percentage of micronuclei than the reference population. These differences between populations were probably caused by an overall decreased fitness of mussels from the contaminated site due to genetic drift and by an enhanced DNA repair mechanism due to adaptation to pollution in the source habitat. Overall, the combination of the three biomarkers provided sufficient information on the impact of both treated and non-treated municipal wastewater on the genetics of zebra mussels at different levels of biological organization.rnIn my thesis, I could show that the newly established marker set of six microsatellite loci provided reliable and informative data for population genetic analyses of D. polymorpha. The adaptation of the analyzed zebra mussel populations to the local conditions of their habitat had a strong influence on their genetic constitution. We found evidence that the different genetic constitutions of two populations had influenced the outcome of our ecotoxicological experiment. Overall, the integrated approach in biomonitoring gave comprehensive information about the impact of both treated and non-treated municipal wastewater on the genetics of zebra mussels at different levels of biological organization and was well practicable in a first case study.

Microbial formation of nitrous acid and its exchange processes between soils and atmosphere

Salpetrige Säure (HONO) ist eine wichtige Form von reaktivem Stickstoff, die aufgrund ihrer Photolyse zu Stickstoffmonoxid (NO) und dem Hydroxylradikal (OH), sehr kurzlebig ist. Ein genaues Verständnis der Quellen und Senken von HONO ist eine grundlegende Voraussetzung, um dessen Einfluss auf die Umwelt zu beurteilen. Allerdings wird immer noch nach einer starken HONO-Quelle am Tag gesucht und nächtliche HONO-Deposition auf den Boden wurde bisher stets nur postuliert. Diese Dissertation folgt der Zielsetzung die Prozesse der HONO-Aufnahme und Freisetzung von Böden aufzudecken und die zugrunde liegenden Mechanismen zu verstehen.rnUm die Rolle von HONO-Bodenemissionen zu quantifizieren, wurden 17 Böden in einem dynamischen Kammersystem untersucht. Es konnten HONO-Emissionen derselben Größenordnung wie die bereits gut untersuchten NO-Emissionen festgestellt werden. Unerwarteter Weise wurden die stärksten Emissionen bei Böden mit neutralem pH aus ariden und landwirt¬schaftlichen Gebieten beobachtet. Die Temperaturabhängigkeit der Bodenemissionen von HONO und NO führten zu der Annahme einer mikrobiellen Freisetzung von HONO, welche durch Reinkulturexperimente mit dem ammoniumoxidierenden Bakterium Nitrosomonas europaea bestätigt werden konnte. Ein konzeptionelles Model für die Freisetzung reaktiver Stickstoffverbindungen aus Böden in Abhängigkeit des Bodenwassergehaltes wurde um HONO-Emissionen erweitert.rnDurch Nachweise mittels Reinkultur- und Inhibitionsexperimenten konnten weitere Untersuchungen der bakteriellen Freisetzung von HONO aus Böden zeigen, dass innerhalb der bakteriellen Nitrifikation nur ammoniumoxidierende Bakterien zur Emission von HONO fähig sind. Durch kontrolliert initiierte Zelllyse konnte gezeigt werden, dass intrazellulär akkumuliertes Hydroxylamin (NH2OH) für die HONO-Freisetzung verantwortlich sind. Zum ersten Mal wurde NH2OH in der Gasphase nachgewiesen und dass dieses über den gesamten Bodenfeuchtebereich von ammoniumoxidierenden Bakterien freigesetzt wird. Es wurde gezeigt, dass die heterogene Reaktion von NH2OH mit Wasserdampf auf einer Glasperlenoberfläche HONO bildet. Diese Reaktion erklärt die beobachtete Freisetzung von HONO bei niedrigen Bodenfeuchten, da nur dann die Oberfläche zur Reaktion zur Verfügung steht und nicht von Wasser bedeckt ist.rnEine 15N Isotopenmarkierungsmethode wurde entwickelt um isotopenmarkiertes gasförmiges HONO zu messen, was die Untersuchung der Bildungsprozesse von HONO und dessen Rolle in biogeochemischen Zyklen ermöglicht. Die Anwendung dieser neuen Methode auf eine Bodenprobe die mit 15N Harnstoff angereichert und in einem dynamischen Kammersystem untersucht wurde, bestätigt die obigen Ergebnisse einer starken mikrobiellen Beteiligung von Bodenbakterien zur HONO Freisetzung.rnBidirektionale Flüsse von HONO wurden für sechs untersuchte Bodenproben gefunden. Die Richtung der Flüsse hängt dabei vom Umgebungsmischungsverhältnis von HONO und dem Bodenwassergehalt ab. Eine wichtige Größe, die die bidirektionalen Flüsse von HONO beschreibt, ist das „Ökosystem spezifische Kompensationsmischungsverhältnis von HONO“, χcomp. Dieser neue Begriff wurde definiert und eingeführt, da die verschiedenen in den Bodenaustausch von HONO involvierten Prozesse nicht mit dem klassischen Kompensationspunktkonzept kompatibel sind. Die Untersuchungen bestätigen neueste Feldbeobachtungen, dass HONO, welches bei hohen Umgebungsmischungsverhältnissen vom Boden adsorbiert wird, bei niedrigen Mischungsverhält-nissen wieder vom Boden desorbiert wird. Folglich wird nächtlich akkumuliertes HONO tagsüber in eine Quelle für HONO umgewandelt. Vier Prozesse - Verteilung von HONO zwischen Gas- und Flüssigphase nach Henrys Gesetz, bakterielle HONO Bildung aus NH2OH, Adsorption und Desorption von HONO - und deren Dominanz in speziellen Bodenfeuchtebereichen wurden identifiziert. Dadurch wurde ein konzeptionelles Model für die Prozesse, die in Aufnahme und Freisetzung von HONO aus Böden involviert sind, als Funktion der Bodenfeuchte entwickelt.rnZusammenfassend hat diese Dissertation die entscheidenden Prozesse im Austausch von HONO zwischen Boden und Atmosphäre aufgeklärt und den der bakteriellen HONO Bildung zugrunde liegenden Mechanismus aufgedeckt. Es konnte gezeigt werden, dass Böden sowohl eine wichtige Quelle als auch eine Senke für HONO sind und sollten folglich in zukünftigen Feldmessungen stärker berücksichtigt werden.rn

Understanding of stuck fermentations : investigations on the relationship between the microbial diversity and chemical composition of must

Das Ziel dieser Arbeit war es, mehr Informationen über unkonventionelle Gründe für Gärstockungen zu gewinnen und neue Wege zu finden, diese zu überwinden. Mikrobielle Sukzession und die chemische Zusammensetzung bei der Gärung wurden in zwei aufeinander folgenden Jahren in einem Weingut von der oberen Mosel in Deutschland studiert. Es gab keinen Hinweis darauf, dass die isolierten Bakterienspezies oder chemischen Komponenten von Most und Jungwein an schleppenden oder stockenden Gärungen beteiligt waren. Ferner konnte während dieser Arbeit gezeigt werden, dass Saccharomyces bayanus die dominierende Weinhefe in diesem Weingut war statt der klassischen und bekannten Weinhefe Saccharomyces cerevisiae. Während der Gärstockung konnte ein Dreifach-Hybrid Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus wachsen, Saccharomyces bayanus ersetzen und die Gärung beenden. Beide isolierten Hefestämme Saccharomyces bayanus Stamm HL 77 und der Dreifach-Hybrid Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus Stamm HL 78 konnten Glucose und Fructose von Anfang an verwerten und konnten bei niedrigen Temperaturen von 15 °C und in der Abwesenheit von Hefe-verwertbarem Stickstoff in Form von Ammonium wachsen, solange Aminosäuren im Medium vorhanden waren, im Gegensatz zu einer kommerziellen Saccharomyces cerevisiae-Starterkultur. Chemische Untersuchungen ergaben, dass Hefe-verwertbarer Stickstoff in dem kooperierenden Weingut mit einem Maximum von 160 mg/l zu Beginn der Gärung vorhanden war und auf 40 mg/L verringert war nach zwei Wochen. Aus diesem Grund sind beide isolierten Hefestämme interessant als Starterkulturen in diesem Weingut und dies kann neben der niedrigen Temperatur im Keller auch ein Grund sein, warum Saccharomyces cerevisiae nicht die dominierende Weinhefe in diesem Fall ist. Der Dreifach-Hybrid Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus Stamm HL 78 ist in der Lage, Fructose noch effizienter zu nutzen als Saccharomyces bayanus Stamm HL 77 und ist weniger abhängig von der Aminosäurekonzentration. Dieser Stamm wurde bereits erfolgreich bei diesem Projekt eingesetzt, um eine Gärstockung in dem kooperierenden Weingut zu beheben. Es ist bekannt, dass Saccharomyces-Hybride in der Weinherstellung vorkommen aber ihre Rolle bei der Überwindung von Gärstockungen wurde bisher noch nicht beschrieben. Diese Ergebnisse sind nützlich, um Gärstockungen zu vermeiden oder zu überwinden mit der selektiven Verwendung dieser Hefestämme in verschiedenen Stadien der Gärung. Das kooperierende Weingut, welches im oberen Qualitätssegment platziert ist, hatte jedes Jahr Probleme mit Gärstockungen. Daher ist die Anwendung der Dreifach-Hybriden Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus Stamm HL 78 eine große Chance, Gärstockungen und finanzielle Verluste ohne kommerzielle Starterkulturen oder andere übliche Praktiken, die zu einer Veränderung des Aromaprofils führen können, zu vermeiden. Die beschriebenen Untersuchungen stellen ein Modell dar, um Gärstockungen auch in anderen Weingütern, die Spontangärungen anwenden, zu überwinden.

Implementation of enhanced biological phosphorus removal (ebpr) wastewater treatment processes enriched with different microbial communities

The EBPR (Enhanced Biological Phosphorus Removal) is a type of secondary treatment in WWTPs (WasteWater Treatment Plants), quite largely used in full-scale plants worldwide. The phosphorus occurring in aquatic systems in high amounts can cause eutrophication and consequently the death of fauna and flora. A specific biomass is used in order to remove the phosphorus, the so-called PAOs (Polyphosphate Accumulating Organisms) that accumulate the phosphorus in form of polyphosphate in their cells. Some of these organisms, the so-called DPAO (Denitrifying Polyphosphate Accumulating Organisms) use as electron acceptor the nitrate or nitrite, contributing in this way also to the removal of these compounds from the wastewater, but there could be side reactions leading to the formation of nitrous oxides. The aim of this project was to simulate in laboratory scale a EBPR, acclimatizing and enriching the specialized biomass. Two bioreactors were operated as Sequencing Batch Reactors, one enriched in Accumulibacter, the other in Tetrasphaera (both PAOs): Tetrasphaera microorganisms are able to uptake aminoacids as carbon source, Accumulibacter uptake organic carbon (volatile fatty acids, VFA). In order to measure the removal of COD, phosphorus and nitrogen-derivate compounds, different analysis were performed: spectrophotometric measure of phosphorus, nitrate, nitrite and ammonia concentrations, TOC (Total Organic Carbon, measuring the carbon consumption), VFA via HPLC (High Performance Liquid Chromatography), total and volatile suspended solids following standard methods APHA, qualitative microorganism population via FISH (Fluorescence In Situ Hybridization). Batch test were also performed to monitor the NOx production. Both specialized populations accumulated as a result of SBR operations; however, Accumulibacter were found to uptake phosphates at higher extents. Both populations were able to remove efficiently nitrates and organic compounds occurring in the feeding. The experimental work was carried out at FCT of Universidade Nova de Lisboa (FCT-UNL) from February to July 2014.

The role of the interplay between polymer architecture and bacterial surface properties on the microbial adhesion to polyoxazoline-based ultrathin films

Surface platforms were engineered from poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL-g-PMOXA) copolymers to study the mechanisms involved in the non-specific adhesion of Escherichia coli (E. coli) bacteria. Copolymers with three different grafting densities (PMOXA chains/Lysine residue of 0.09, 0.33 and 0.56) were synthesized and assembled on niobia (Nb O ) surfaces. PLL-modified and bare niobia surfaces served as controls. To evaluate the impact of fimbriae expression on the bacterial adhesion, the surfaces were exposed to genetically engineered E. coli strains either lacking, or constitutively expressing type 1 fimbriae. The bacterial adhesion was strongly influenced by the presence of bacterial fimbriae. Non-fimbriated bacteria behaved like hard, charged particles whose adhesion was dependent on surface charge and ionic strength of the media. In contrast, bacteria expressing type 1 fimbriae adhered to the substrates independent of surface charge and ionic strength, and adhesion was mediated by non-specific van der Waals and hydrophobic interactions of the proteins at the fimbrial tip. Adsorbed polymer mass, average surface density of the PMOXA chains, and thickness of the copolymer films were quantified by optical waveguide lightmode spectroscopy (OWLS) and variable-angle spectroscopic ellipsometry (VASE), whereas the lateral homogeneity was probed by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Streaming current measurements provided information on the charge formation of the polymer-coated and the bare niobia surfaces. The adhesion of both bacterial strains could be efficiently inhibited by the copolymer film only with a grafting density of 0.33 characterized by the highest PMOXA chain surface density and a surface potential close to zero.

Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses

The lower intestine of adult mammals is densely colonized with nonpathogenic (commensal) microbes. Gut bacteria induce protective immune responses, which ensure host-microbial mutualism. The continuous presence of commensal intestinal bacteria has made it difficult to study mucosal immune dynamics. Here, we report a reversible germ-free colonization system in mice that is independent of diet or antibiotic manipulation. A slow (more than 14 days) onset of a long-lived (half-life over 16 weeks), highly specific anticommensal immunoglobulin A (IgA) response in germ-free mice was observed. Ongoing commensal exposure in colonized mice rapidly abrogated this response. Sequential doses lacked a classical prime-boost effect seen in systemic vaccination, but specific IgA induction occurred as a stepwise response to current bacterial exposure, such that the antibody repertoire matched the existing commensal content.

Child and adolescent psychiatric genetics

The current status of child and adolescent psychiatric genetics appears promising in light of the initiation of genome-wide association studies (GWAS) for diverse polygenic disorders and the molecular elucidation of monogenic Rett syndrome, for which recent functional studies provide hope for pharmacological treatment strategies. Within the last 50 years, tremendous progress has been made in linking genetic variation to behavioral phenotypes and psychiatric disorders. We summarize the major findings of the Human Genome Project and dwell on largely unsuccessful candidate gene and linkage studies. GWAS for the first time offer the possibility to detect single nucleotide polymorphisms and copy number variants without a priori hypotheses as to their molecular etiology. At the same time it is becoming increasingly clear that very large sample sizes are required in order to enable genome wide significant findings, thus necessitating further large-scaled ascertainment schemes for the successful elucidation of the molecular genetics of childhood and adolescent psychiatric disorders. We conclude by reflecting on different scenarios for future research into the molecular basis of early onset psychiatric disorders. This review represents the introductory article of this special issue of the European Child and Adolescent Psychiatry.

Genetics of male nuptial colour divergence between sympatric sister species of a Lake Victoria cichlid fish

The hypothesis of sympatric speciation by sexual selection has been contentious. Several recent theoretical models of sympatric speciation by disruptive sexual selection were tailored to apply to African cichlids. Most of this work concludes that the genetic architecture of female preference and male trait is a key determinant of the likelihood of disruptive sexual selection to result in speciation. We investigated the genetic architecture controlling male nuptial colouration in a sympatric sibling species pair of cichlid fish from Lake Victoria, which differ conspicuously in male colouration and female mating preferences for these. We estimated that the difference between the species in male nuptial red colouration is controlled by a minimum number of two to four genes with significant epistasis and dominance effects. Yellow colouration appears to be controlled by one gene with complete dominance. The two colours appear to be epistatically linked. Knowledge on how male colouration segregates in hybrid generations and on the number of genes controlling differences between species can help us assess whether assumptions made in simulation models of sympatric speciation by sexual selection are realistic. In the particular case of the two sister species that we studied a small number of genes causing major differences in male colouration may have facilitated the divergence in male colouration associated with speciation.