Complex materials via colloidal crystallization

The work presented in this thesis deals with complex materials, which were obtained by self-assembly of monodisperse colloidal particles, also called colloidal crystallization. Two main fields of interest were investigated, the first dealing with the fabrication of colloidal monolayers and nanostructures, which derive there from. The second turned the focus on the phononic properties of colloidal particles, crystals, and glasses. For the fabrication of colloidal monolayers a method is introduced, which is based on the sparse distribution of dry colloidal particles on a parent substrate. In the ensuing floating step the colloidal monolayer assembles readily at the three-phase-contact line, giving a 2D hexagonally ordered film under the right conditions. The unique feature of this fabrication process is an anisotropic shrinkage, which occurs alongside with the floating step. This phenomenon is exploited for the tailored structuring of colloidal monolayers, leading to designed hetero-monolayers by inkjet printing. Furthermore, the mechanical stability of the floating monolayers allows the deposition on hydrophobic substrates, which enables the fabrication of ultraflat nanostructured surfaces. Densely packed arrays of crescent shaped nanoparticles have also been synthesized. It is possible to stack those arrays in a 3D manner allowing to mutually orientate the individual layers. In a step towards 3D mesoporous materials a methodology to synthesize hierarchically structured inverse opals is introduced. The deposition of colloidal particles in the free voids of a host inverse opal allows for the fabrication of composite inverse opals on two length scales. The phononic properties of colloidal crystals and films are characterized by Brillouin light scattering (BLS). At first the resonant modes of colloidal particles consisting of polystyrene, a copolymer of methylmethacrylate and butylacrylate, or of a silica core-PMMA shell topography are investigated, giving insight into their individual mechanical properties. The infiltration of colloidal films with an index matching liquid allows measuring the phonon dispersion relation. This leads to the assignment of band gaps to the material under investigation. Here, two band gaps could be found, one originating from the fcc order in the colloidal crystal (Bragg gap), the other stemming from the vibrational eigenmodes of the colloidal particles (hybridization gap).

Dynamic wetting of complex liquids

A simple dependency between contact angle θ and velocity or surface tension has been predicted for the wetting and dewetting behavior of simple liquids. According to the hydrodynamic theory, this dependency was described by Cox and Voinov as θ ∼ Ca^(1/3) (Ca: Capillary number). For more complex liquids like surfactant solutions, this prediction is not directly given.rnHere I present a rotating drum setup for studying wetting/dewetting processes of surfactant solutions on the basis of velocity-dependent contact angle measurements. With this new setup I showed that surfactant solutions do not follow the predicted Cox-Voinov relation, but showed a stronger contact angle dependency on surface tension. All surfactants independent of their charge showed this difference from the prediction so that electrostatic interactions as a reason could be excluded. Instead, I propose the formation of a surface tension gradient close to the three-phase contact line as the main reason for the strong contact angle decrease with increasing surfactant concentration. Surface tension gradients are not only formed locally close to the three-phase contact line, but also globally along the air-liquid interface due to the continuous creation/destruction of the interface by the drum moving out of/into the liquid. By systematically hindering the equilibration routes of the global gradient along the interface and/or through the bulk, I was able to show that the setup geometry is also important for the wetting/dewetting of surfactant solutions. Further, surface properties like roughness or chemical homogeneity of the wetted/dewetted substrate influence the wetting/dewetting behavior of the liquid, i. e. the three-phase contact line is differently pinned on rough/smooth or homogeneous/inhomogeneous surfaces. Altogether I showed that the wetting/dewetting of surfactant solutions did not depend on the surfactant type (anionic, cationic, or non-ionic) but on the surfactant concentration and strength, the setup geometry, and the surface properties.rnSurfactants do not only influence the wetting/dewetting behavior of liquids, but also the impact behavior of drops on free-standing films or solutions. In a further part of this work, I dealt with the stability of the air cushion between drop and film/solution. To allow coalescence between drop and substrate, the air cushion has to vanish. In the presence of surfactants, the vanishing of the air is slowed down due to a change in the boundary condition from slip to no-slip, i. e. coalescence is suppressed or slowed down in the presence of surfactant.

Das GAF-Domänen-Protein NreA : ein neuartiger Nitratrezeptor aus Staphylococcus carnosus

Staphylococcus carnosus ist ein fakultativ anaerobes Bakterium, das aerobe Atmung, anaerobe Nitratatmung und Gärungsstoffwechsel betreiben kann. Die Expression des Nitratstoffwechsels wird durch das Dreikomponentensystem NreABC reguliert.rnUnter anaeroben Bedingungen besitzt die Sensorhistidinkinase NreB in ihrer PAS-Domäne ein [Fe4S4]2+-Cluster. Das aktive (anaerobe) [Fe4S4]2+-NreB überträgt nach Autophosphorylierung die Phosphorylgruppe auf den Antwortregulator NreC, welcher dann die Expression der Gene der Nitratatmung aktiviert. Nitrat wirkt mit Hilfe des NreA-Proteins auf diese Gene induzierend. Im Rahmen der vorliegenden Arbeit wurde gezeigt, dass NreA ein GAF-Domänen-Protein und ein neuartiger Nitratrezeptor ist.rnDie Natur von NreA als GAF-Domänen-Protein bestätigte sich beim Vergleich der Kristallstruktur mit denen anderer GAF-Domänen. GAF-Domänen sind weit verbreitet und binden typischer Weise kleine Moleküle. Als physiologischer Ligand von NreA zeigte sich Nitrat, das innerhalb einer definierten Bindetasche gebunden wird. NreA bindet vermutlich in dimerer Form an dimeres NreB und inhibiert dadurch die Phosphorylierung der Sensorhistidinkinase NreB. Die Interaktion von NreA mit NreB wurde in vivo durch BACTH-Messungen und sowohl in vivo als auch in vitro durch Cross-Linking Experimente gezeigt. Nitrat reduziert den Ergebnissen nach die Interaktion von NreA mit NreB.rnDurch Sequenzvergleiche von NreA mit Homologen wurden konservierte Aminosäuren identifiziert. Über gerichtete Mutagenese wurden 25 NreA-Varianten hergestellt und bezüglich ihres Verhaltens in Abhängigkeit von Nitrat in narG-lip-Reportergenstudien getestet. Anhand ihres Phänotyps wurden sie als Wildtyp, NreA- und NreABC-Mutanten klassifiziert. Die Nitratbindetasche war in sechs Fällen betroffen. Die Phänotypen der Mutationen in der Peripherie lassen sich mit Auswirkungen auf die vermutete Konformationsänderung oder auf die Interaktion mit NreB erklären. Mutationen von konservierten, oberflächenexponierten Resten führten vermehrt zu NreA/ON-Varianten. Es ließen sich Bereiche auf der Proteinoberfläche identifizieren, die für NreA/NreA- oder NreA/NreB-Interaktionen wichtig sein könnten.rnDie Untersuchungen zeigten, dass NreA mit NreB interagiert und dass dadurch ein NreA/NreB-Sensorkomplex für die gemeinsame Erkennung von Nitrat und Sauerstoff gebildet wird.

Nanofiber-based spectroscopy of organic molecules

This thesis reports on the experimental realization of nanofiber-based spectroscopy of organic molecules. The light guided by subwavelength diameter optical nanfibers exhibits a pronounced evanescent field surrounding the fiber which yields high excitation and emission collection efficiencies for molecules on or near the fiber surface.rnThe optical nanofibers used for the experiments presented in this thesis are realized as thernsub-wavelength diameter waist of a tapered optical fiber (TOF). The efficient transfer of thernlight from the nanofiber waist to the unprocessed part of the TOF depends critically on therngeometric shape of the TOF transitions which represent a nonuniformity of the TOF. Thisrnnonuniformity can cause losses due to coupling of the fundamental guided mode to otherrnmodes which are not guided by the taper over its whole length. In order to quantify the lossrnfrom the fundamental mode due to tapering, I have solved the coupled local mode equationsrnin the approximation of weak guidance for the three layer system consisting of fiber core andrncladding as well as the surrounding vacuum or air, assuming the taper shape of the TOFsrnused for the experiments presented in this thesis. Moreover, I have empirically studied therninfluence of the TOF geometry on its transmission spectra and, based on the results, I haverndesigned a nanofiber-waist TOF with broadband transmission for experiments with organicrnmolecules.rnAs an experimental demonstration of the high sensitivity of nanofiber-based surface spectroscopy, I have performed various absorption and fluorescence spectroscopy measurements on the model system 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA). The measured homogeneous and inhomogeneous broadening of the spectra due to the interaction of the dielectric surface of the nanofiber with the surface-adsorbed molecules agrees well with the values theoretically expected and typical for molecules on surfaces. Furthermore, the self-absorption effects due to reasorption of the emitted fluorescence light by circumjacent surface-adsorbed molecules distributed along the fiber waist have been analyzed and quantified. With time-resolved measurements, the reorganization of PTCDA molecules to crystalline films and excimers can be observed and shown to be strongly catalyzed by the presence of water on the nanofiber surface. Moreover, the formation of charge-transfer complexes due to the interaction with localized surface defects has been studied. The collection efficiency of the molecular emission by the guided fiber mode has been determined by interlaced measurements of absorption and fluorescence spectra to be about 10% in one direction of the fiber.rnThe high emission collection efficiency makes optical nanofibers a well-suited tool for experiments with dye molecules embedded in small organic crystals. As a first experimental realization of this approach, terrylene-doped para-terphenyl crystals attached to the nanofiber-waist of a TOF have been studied at cryogenic temperatures via fluorescence and fluorescence excitation spectroscopy. The statistical fine structure of the fluorescence excitation spectrum for a specific sample has been observed and used to give an estimate of down to 9 molecules with center frequencies within one homogeneous width of the laser wavelength on average for large detunings from resonance. The homogeneous linewidth of the transition could be estimated to be about 190MHz at 4.5K.

[SPECT/CT diagnostics for skeletal infections]

CLINICAL/METHODICAL ISSUE: Skeletal infections are often a diagnostic and clinical challenge. STANDARD RADIOLOGICAL METHODS: Nuclear imaging modalities used in the diagnostic workup of acute and chronic skeletal infections include three-phase bone scintigraphy and scintigraphy with labelled leucocytes. METHODICAL INNOVATIONS: The introduction of hybrid technologies, such as single photon emission computed tomography/computed tomography (SPECT/CT) has dramatically changed nuclear medical imaging of infections. PERFORMANCE: In general SPECT/CT leads to a considerably more accurate diagnosis than planar or SPECT imaging. ACHIEVEMENTS: Given the integrated acquisition of metabolic, functional and morphological information, SPECT/CT has increased in particular the specificity of three-phase skeletal scanning and scintigraphy with labeled leucocytes.

The treatment of spasticity with Delta9-tetrahydrocannabinol in persons with spinal cord injury

STUDY DESIGN: Open label study to determine drug dose for a randomized double-blind placebo-controlled parallel study. OBJECTIVES: To assess the efficacy and side effects of oral Delta(9)-tetrahydrocannabinol (THC) and rectal THC-hemisuccinate (THC-HS) in SCI patients. SETTING: REHAB Basel, Switzerland. METHOD: Twenty-five patients with SCI were included in this three-phase study with individual dose adjustment, each consisting of 6 weeks. Twenty-two participants received oral THC open label starting with a single dose of 10 mg (Phase 1, completed by 15 patients). Eight subjects received rectal THC-HS (Phase 2, completed by seven patients). In Phase 3, six patients were treated with oral THC and seven with placebo. Major outcome parameters were the spasticity sum score (SSS) using the Modified Ashworth Scale (MAS) and self-ratings of spasticity. RESULTS: Mean daily doses were 31 mg with THC and 43 mg with THC-HS. Mean SSS for THC decreased significantly from 16.72 (+/-7.60) at baseline to 8.92 (+/-7.14) on day 43. Similar improvement was seen with THC-HS. We observed a significant improvement of SSS with active drug (P=0.001) in the seven subjects who received oral THC in Phase 1 and placebo in Phase 3. Major reasons for drop out were increase of pain and psychological side effects. CONCLUSION: THC is an effective and safe drug in the treatment of spasticity. At least 15-20 mg per day were needed to achieve a therapeutic effect.

Atovaquone inhibits the glucuronidation and increases the plasma concentrations of zidovudine

The pharmacokinetic interaction between atovaquone, a 1,4-hydroxynaphthoquinone, and zidovudine was examined in an open, randomized, three-phase crossover study in 14 patients infected with human immunodeficiency virus. Atovaquone (750 mg every 12 hours) and zidovudine (200 mg every 8 hours) were given orally alone and in combination. Atovaquone significantly increased the area under the zidovudine concentration-time curve (AUC) (1.82 +/- 0.62 micrograms.hr/ml versus 2.39 +/- 0.68 micrograms.hr/ml; p < 0.05) and decreased the oral clearance of zidovudine (2029 +/- 666 ml/min versus 1512 +/- 464 ml/min; p < 0.05). In contrast, atovaquone tended to decrease the AUC of zidovudine-glucuronide (7.31 +/- 1.51 micrograms.hr/ml versus 6.89 +/- 1.42 micrograms.hr/ml; p < 0.1) and significantly decreased the ratio of AUC zidovudine-glucuronide/AUC zidovudine (4.48 +/- 1.94 versus 3.12 +/- 1.1; p < 0.05). The maximum concentration of zidovudine-glucuronide was significantly lowered by atovaquone (5.7 +/- 1.5 versus 4.57 +/- 0.97 micrograms/ml; p < 0.05). Zidovudine had no effect on the pharmacokinetic disposition of atovaquone. Atovaquone appears to increase the AUC of zidovudine by inhibiting the glucuronidation of zidovudine.

Methodological approach to the first and second lactate threshold in incremental cardiopulmonary exercise testing

Determination of an 'anaerobic threshold' plays an important role in the appreciation of an incremental cardiopulmonary exercise test and describes prominent changes of blood lactate accumulation with increasing workload. Two lactate thresholds are discerned during cardiopulmonary exercise testing and used for physical fitness estimation or training prescription. A multitude of different terms are, however, found in the literature describing the two thresholds. Furthermore, the term 'anaerobic threshold' is synonymously used for both, the 'first' and the 'second' lactate threshold, bearing a great potential of confusion. The aim of this review is therefore to order terms, present threshold concepts, and describe methods for lactate threshold determination using a three-phase model with reference to the historical and physiological background to facilitate the practical application of the term 'anaerobic threshold'.

Kalman Filter approaches on crane swing

The purpose of this study is to explore a Kalman Filter approach to estimating swing of crane-suspended loads. Measuring real-time swing is needed to implement swing damping control strategies where crane joints are used to remove energy from a swinging load. The typical solution to measuring swing uses an inertial sensor attached to the hook block. Measured hook block twist is used to resolve the other two sensed body rates into tangential and radial swing. Uncertainty in the twist measurement leads to inaccurate tangential and radial swing calculations and ineffective swing damping. A typical mitigation approach is to bandpass the inertial sensor readings to remove low frequency drift and high frequency noise. The center frequency of the bandpass filter is usually designed to track the load length and the pass band width set to trade off performance with damping loop gain. The Kalman Filter approach developed here allows all swing motions (radial, tangential and twist) to be measured without the use of a bandpass filter. This provides an alternate solution for swing damping control implementation. After developing a Kalman Filter solution for a two-dimensional swing scenario, the three-dimensional system is considered where simplifying assumptions, suggested by the two-dimensional study, are exploited. One of the interesting aspects of the three-dimensional study is the hook block twist model. Unlike the mass-independence of a pendulum's natural frequency, the twist natural frequency depends both on the pendulum length and the load’s mass distribution. The linear Kalman Filter is applied to experimental data demonstrating the ability to extract the individual swing components for complex motions. It should be noted that the three-dimensional simplifying assumptions preclude the ability to measure two "secondary" hook block rotations. The ability to segregate these motions from the primary swing degrees of freedom was illustrated in the two-dimensional study and could be included into the three-dimensional solution if they were found to be important for a particular application.

INVESTIGATING THE ROLE OF THE CONTACT LINE IN HETEROGENEOUS NUCLEATION WITH HIGH SPEED IMAGING

While nucleation of solids in supercooled liquids is ubiquitous [15, 65, 66], surface crystallization, the tendency for freezing to begin preferentially at the liquid-gas interface, has remained puzzling [74, 18, 68, 69, 51, 64, 72, 16]. Here we employ high-speed imaging of supercooled water drops to study the phenomenon of heterogeneous surface crystallization. Our geometry avoids the "point-like contact" of prior experiments by providing a simple, symmetric contact line (triple line defined by the substrate-liquid-air interface) for a drop resting on a homogeneous silicon substrate. We examine three possible mechanisms that might explain these laboratory observations: (i) Line Tension at the triple line, (ii) Thermal Gradients within the droplets and (iii) Surface Texture. In our first study we record nearly perfect spatial uniformity in the immersed (liquid-substrate) region and, thereby, no preference for nucleation at the triple line. In our second study, no influence of thermal gradients on the preference for freezing at the triple line was observed. Motivated by the conjectured importance of line tension (τ) [1, 66] for heterogeneous nucleation, we also searched for evidence of a transition to surface crystallization at length scales on the order of δ ∼ τ/σ, where σ is the surface tension [14]; poorly constrained τ [49] leads to δ ranging from microns to nanometers. We demonstrate that nano-scale texture causes a shift in the nucleation to the three-phase contact line, while micro-scale texture does not. The possibility of a critical length scale has implications for the effectiveness of nucleation catalysts, including formation of ice in atmospheric clouds [7].

Virus purification, detection and removal

The biopharmaceutical industry has a growing demand and an increasing need to improve the current virus purification technologies, especially as more and more vaccines are produced from cell-culture derived virus particles. Downstream purification strategies can be expensive and account for 70% of the overall manufacturing costs. The economic pressure and purification processes can be particularly challenging when the virus to be purified is small, as in our model virus, porcine parvovirus (PPV). Our efforts are focused on designing an easy, economical, scalable and efficient system for virus purification, and we focused on aqueous two-phase systems. Industry acceptable standards for virus vaccine recovery can be as low as 30% due to demand of high final titer, virus transduction inhibitors and presence of empty or defective virus capsids as impurities. We have overcome these shortcomings by recovering a high 64% of infectious virus using an aqueous two-phase system. We used high molecular weight polymer and citrate salt to achieve a good yield and eliminated the major contaminant bovine serum albumin. Viruses are also studied for ensuring pure and safe drinking water. Low pressure microfiltrations are continuously being investigated for water filters as they allow high permeate flux and low fouling. Viruses such as PPV are small enough to pass through the microporous membranes. Control of viruses in water is crucial for public health and we have designed an affinity based membrane filter to capture virus. Nanofibers have a high surface to volume ratio providing a highly accessible surface area for virus adsorption. Chitosan an insoluble, biocompatible and biodegradable polymer was used for adsorbing trimer peptide WRW. About 0.2 μmoles of cysteine terminal WRW peptide was conjugated to amine terminal chitosan using maleimide conjugation chemistry. We achieved 90-99% virus removal from water adjusted to a neutral pH. The virus removal from affinity based chitosan was attributed to electrostatic and hydrophobic driven binding effect.

Japanese-US common-arm analysis of paclitaxel plus carboplatin in advanced non-small-cell lung cancer: a model for assessing population-related pharmacogenomics

PURPOSE To explore whether population-related pharmacogenomics contribute to differences in patient outcomes between clinical trials performed in Japan and the United States, given similar study designs, eligibility criteria, staging, and treatment regimens. METHODS We prospectively designed and conducted three phase III trials (Four-Arm Cooperative Study, LC00-03, and S0003) in advanced-stage, non-small-cell lung cancer, each with a common arm of paclitaxel plus carboplatin. Genomic DNA was collected from patients in LC00-03 and S0003 who received paclitaxel (225 mg/m(2)) and carboplatin (area under the concentration-time curve, 6). Genotypic variants of CYP3A4, CYP3A5, CYP2C8, NR1I2-206, ABCB1, ERCC1, and ERCC2 were analyzed by pyrosequencing or by PCR restriction fragment length polymorphism. Results were assessed by Cox model for survival and by logistic regression for response and toxicity. Results Clinical results were similar in the two Japanese trials, and were significantly different from the US trial, for survival, neutropenia, febrile neutropenia, and anemia. There was a significant difference between Japanese and US patients in genotypic distribution for CYP3A4*1B (P = .01), CYP3A5*3C (P = .03), ERCC1 118 (P < .0001), ERCC2 K751Q (P < .001), and CYP2C8 R139K (P = .01). Genotypic associations were observed between CYP3A4*1B for progression-free survival (hazard ratio [HR], 0.36; 95% CI, 0.14 to 0.94; P = .04) and ERCC2 K751Q for response (HR, 0.33; 95% CI, 0.13 to 0.83; P = .02). For grade 4 neutropenia, the HR for ABCB1 3425C-->T was 1.84 (95% CI, 0.77 to 4.48; P = .19). CONCLUSION Differences in allelic distribution for genes involved in paclitaxel disposition or DNA repair were observed between Japanese and US patients. In an exploratory analysis, genotype-related associations with patient outcomes were observed for CYP3A4*1B and ERCC2 K751Q. This common-arm approach facilitates the prospective study of population-related pharmacogenomics in which ethnic differences in antineoplastic drug disposition are anticipated.

Rhyming the National Spirit: Taras Shevchenko and Ilia Chavchavadze

The paper is a comparative inquiry into the roles of Ilia Chavchavadze (1837-1907) and Taras Shevchenko (1818-1861) as national poets and anti-colonial (anti-Tsarist) intellectuals within the context of their respective national traditions (Georgia and Ukraine). During the period of their activity (19th and the beginning of 20th century) both Ukraine and Georgia were under Tsarist imperial rule, albeit the two poets lived in different periods of Russian empire history. Through their major works, each called on their communities to ‘awaken’ and ‘revolt’ against oppression, rejected social apathy caused by Tsarist subjugation and raised awareness about the historical past of their nations. The non-acceptance of present and belief in an independent future was one of the dominant themes in the poetry and prose of both. Their contemporary importance is illustrated in political discourse both after Orange Revolution in Ukraine (2004), and Rose Revolution in Georgia (2003) where both poets are referred “as founding fathers of national ideology”, the history textbooks alluding to them as “symbols of anti-colonial resistance”. To this day, however, there has been surprisingly little academic writing in the West endeavoring to compare the works and activities of the two poets and their impact on national mobilization in Tsarist Ukraine and Georgia, even though their countries are often mentioned in a same breath by commentators on contemporary culture and politics. The paper attempts to fill this gap and tries to understand the relationship between literature and social mobilization in 19th century Russian Empire. By reflecting on Taras Shevchenko’s and Ilia Chavchavadze’s poetry, prose and social activism, I will try to explain how in different periods of Russian imperial history, the two poets helped to develop a modern form of political belonging among their compatriots and stimulated an anti-colonial mobilization with different political outcomes. To theorize on the role of poets and novelists in anti-colonial national movement, I will reflect on the writings of Benedict Anderson (1991), John Hutchinson (1994; 1999), Rory Finnin (2005; 2011) and problematize Miroslav Hroch’s (1996) three phase model of the development of national movements. Overall, the paper would aim to show the importance of, what John Hutchinson called, ‘cultural nationalists’ in understanding contemporary nationalist discourse in Georgian and Ukrainian societies.

Comparative carbon cycle dynamics of the present and last interglacial

Changes in temperature and carbon dioxide during glacial cycles recorded in Antarctic ice cores are tightly coupled. However, this relationship does not hold for interglacials. While climate cooled towards the end of both the last (Eemian) and present (Holocene) interglacials, CO₂ remained stable during the Eemian while rising in the Holocene. We identify and review twelve biogeochemical mechanisms of terrestrial (vegetation dynamics and CO₂ fertilization, land use, wild fire, accumulation of peat, changes in permafrost carbon, subaerial volcanic outgassing) and marine origin (changes in sea surface temperature, carbonate compensation to deglaciation and terrestrial biosphere regrowth, shallow-water carbonate sedimentation, changes in the soft tissue pump, and methane hydrates), which potentially may have contributed to the CO₂ dynamics during interglacials but which remain not well quantified. We use three Earth System Models (ESMs) of intermediate complexity to compare effects of selected mechanisms on the interglacial CO₂ and δ¹³ CO₂ changes, focusing on those with substantial potential impacts: namely carbonate sedimentation in shallow waters, peat growth, and (in the case of the Holocene) human land use. A set of specified carbon cycle forcings could qualitatively explain atmospheric CO₂ dynamics from 8ka BP to the pre-industrial. However, when applied to Eemian boundary conditions from 126 to 115 ka BP, the same set of forcings led to disagreement with the observed direction of CO₂ changes after 122 ka BP. This failure to simulate late-Eemian CO₂ dynamics could be a result of the imposed forcings such as prescribed CaCO₃ accumulation and/or an incorrect response of simulated terrestrial carbon to the surface cooling at the end of the interglacial. These experiments also reveal that key natural processes of interglacial CO₂ dynamics eshallow water CaCO₃ accumulation, peat and permafrost carbon dynamics are not well represented in the current ESMs. Global-scale modeling of these long-term carbon cycle components started only in the last decade, and uncertainty in parameterization of these mechanisms is a main limitation in the successful modeling of interglacial CO₂ dynamics.

AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland.

Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangements.