The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates.

Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds to the early conservation model or the hourglass model, respectively. Conflicting results have been reported, but in recent studies of animal transcriptomes the hourglass model has been favored. Studies usually report descriptive statistics calculated for all genes over all developmental time points. This introduces dependencies between the sets of compared genes and may lead to biased results. Here we overcome this problem using an alternative modular analysis. We used the Iterative Signature Algorithm to identify distinct modules of genes co-expressed specifically in consecutive stages of zebrafish development. We then performed a detailed comparison of several gene properties between modules, allowing for a less biased and more powerful analysis. Notably, our analysis corroborated the hourglass pattern at the regulatory level, with sequences of regulatory regions being most conserved for genes expressed in mid-development but not at the level of gene sequence, age, or expression, in contrast to some previous studies. The early conservation model was supported with gene duplication and birth that were the most rare for genes expressed in early development. Finally, for all gene properties, we observed the least conservation for genes expressed in late development or adult, consistent with both models. Overall, with the modular approach, we showed that different levels of molecular evolution follow different patterns of developmental constraints. Thus both models are valid, but with respect to different genomic features.

Glutamatergic and GABAergic energy metabolism measured in the rat brain by (13) C NMR spectroscopy at 14.1 T.

Energy metabolism supports both inhibitory and excitatory neurotransmission processes. This study investigated the specific contribution of astrocytic metabolism to γ-aminobutyric acid (GABA) synthesis and inhibitory GABAergic neurotransmission that remained to be ilucidated in vivo. Therefore, we measured (13) C incorporation into brain metabolites by dynamic (13) C nuclear magnetic resonance spectroscopy at 14.1 T in rats under α-chloralose anaesthesia during infusion of [1,6-(13) C]glucose. The enhanced sensitivity at 14.1 T allowed to quantify incorporation of (13) C into the three aliphatic carbons of GABA non-invasively. Metabolic fluxes were determined with a mathematical model of brain metabolism comprising glial, glutamatergic and GABAergic compartments. GABA synthesis rate was 0.11 ± 0.01 μmol/g/min. GABA-glutamine cycle was 0.053 ± 0.003 μmol/g/min and accounted for 22 ± 1% of total neurotransmitter cycling between neurons and glia. Cerebral glucose oxidation was 0.47 ± 0.02 μmol/g/min, of which 35 ± 1% and 7 ± 1% was diverted to the glutamatergic and GABAergic tricarboxylic acid cycles, respectively. The remaining fraction of glucose oxidation was in glia, where 12 ± 1% of the TCA cycle flux was dedicated to oxidation of GABA. 16 ± 2% of glutamine synthesis was provided to GABAergic neurons. We conclude that substantial metabolic activity occurs in GABAergic neurons and that glial metabolism supports both glutamatergic and GABAergic neurons in the living rat brain. We performed (13) C NMR spectroscopy in vivo at high magnetic field (14.1 T) upon administration of [1,6-(13) C]glucose. This allowed to measure (13) C incorporation into the three aliphatic carbons of GABA in the rat brain, in addition to those of glutamate, glutamine and aspartate. These data were then modelled to determine fluxes of energy metabolism in GABAergic and glutamatergic neurons and glial cells.

Characterising avian haemosporidian communities : ecological factors, parasite persistence and co-infection

Les parasites jouent un rôle clef dans l'évolution des comportements et des traits d'histoire de vie de leurs hôtes. Le parasitisme s'avère parfois dévastateur à l'échelle de population d'hôtes, et peut également altérer certains traits associés à la valeur sélective d'un individu infecté, tels que son succès reproducteur ou encore son taux de mortalité. La coévolution hôte/parasite, qui représente l'une des forces sélectives les plus puissantes dans l'évolution des organismes, peut également conduire les partenaires de l'association parasitaire à s'adapter localement à des environnements hétérogènes. Cette thèse porte sur l'étude de parasites aviaires, du genre Plasmodium, Haemopro- teus et Leucocytozoon (Haemosporidae), naturellement associés à différentes populations de mésanges charbonnières (Parus major) et d'hirondelles des fenêtres (Delichon ur- bicum). Dans un premier temps, nous avons cherché à déterminer comment se distribuent ces parasites au sein de différentes populations hôtes et si ces communautés de parasites sont structurées. Par la suite, la principale question à laquelle nous voulions répondre était de savoir comment ces parasites, et notamment après coexistence de plusieurs lignées génétiques d'Haemosporidae au sein dun même-individu (i.e. co-infection), affectent la physiologie et le succès de reproducteur des hôtes. Nos résultats suggèrent que la distribution des Haemosporidae est principalement gouvernée par la présence d'insectes vecteurs et que la persistance de l'infection chez les hôtes varie en fonction du genre d'Haemosporidae (Chapitre 1-2). Par ailleurs, nous avons trouvé que des lignées de parasite génétiquement distinctes peuvent avoir des effets contrastés sur leurs hôtes. Par exemple, les hôtes exhibent des différences de parasitémie marquées en fonction des lignées de parasites responsable de l'infection. De plus, le succès reproducteur ainsi que la charge parasitaire des mésanges infectées par Plasmodium ou Haemoproteus n'étaient pas affecté par l'infection simultanée avec Leucocytozoon (Chapitre 2-3). Dans le Chapitre 4, j'ai examiné la capacité immunitaire de mésanges charbonnières infectées par des hémosporidies. Les résultats n'ont pas été concluant, et je suggère fortement une réévaluation de ceux-ci dans de futures études. Les mésanges charbonnières ne semblent pas signaler leur statut infectieux par la coloration de leur plumage (Chapitre 5); toutefois, la coloration noire des plumes reflète l'état de stress oxydatif des mésanges, qui dépend lui-même de l'infection parasitaire. La coloration verte pourrait également indiquer la qualité des soins paxentaux délivrés par les mésanges adultes femelles à leurs petits, comme le suggère la corrélation que nous avons observée entre la masse des jeunes d'une nichée et la coloration de leur mère. Les hirondelles capturées en Algérie souffrent plus de l'infection que celles échantillon¬nées en Europe (Chapitre 6). Les similitudes observées entre les communautés de par¬asites affectant les populations européennes et celles des populations nord-africaines suggèrent que la transmission des parasites a lieu lors de la migration vers le sud. A l'instar de nos observations sur les mésanges dans les chapitres 2 et 3, les hirondelles co-infectées ne montrent pas d'altérations de leur condition physique. Cette thèse démontre qu'il existe, au sein des populations de mésanges charbonnières, des interactions antagonistes entre, d'une part, les parasites et leurs hôtes et d'autre part, entre différent parasites. Le résultat de ces interactions antagonistes varie en fonction des espèces et de la zone géographique considérée. Nous avons démontré que les interactions ne suivent pas toujours la théorie, puisque la coevolution qui, en suivant le concept de la virulence, devrait augmenter la charge parasitaire et diminuer la condition physique des hôtes, ne montre pourtant pas d'impact négatif sur les populations de mésanges. Nous pouvons maintenant concentrer nos efforts à la caractérisation des interactions antagonistes. De plus, grâce aux avancées des méthodes moléculaires, nous pouvons suivre et étudier en détails comment ces interactions se manifestent et quels sont leurs effets sur la condition physique des hôtes. - Parasites are key in shaping various behavioural and life-history traits of their hosts. The influence of parasitism on host populations varies from slight to devastating and might influence such parameters as mortality rates or reproductive success. Host-parasite coevolution is one of the most powerful selective forces in evolution and can lead to local adaptation of parasites and hosts in spatially structured environments. In this thesis, I studied haemosporidian parasites in different populations of great tits (Parus major) and house martins (Delichon urbicum). Firstly, I wanted to determine how parasites are distributed and if parasite communities are structured. The main question I wanted to address hereafter was how parasites, and specifically infection with multiple genera of parasites (i.e. co-infection) influenced host physiology and reproductive success. I found that parasite distribution is environmentally driven and could therefore be closely linked to vector prevalence; and that the stability of parasite infection over time is genus-dependent (Chapter 1 - 2). I further found that different haemosporidian lineages might interact differently with their hosts as parasitaemia was strongly lineage-specific and that the presence of Leucocytozoon parasites showed no correlation to Plasmodium or Haemoproteus parasitaemia, nor to great tit reproductive success (Chapter 2-3). In Chapter 4 I examined immune capacity of haemosporidian-infected great tits. The results proved inconclusive, and I strongly suggest re-evaluation hereof in future work. Great tits do not appear to signal parasite infection through plumage colouration (Chapter 5); however, infection did have a link to oxidative stress resistance which is strongly signalled through the black breast stripe, with darker males being more resistant and darker females less resistant. Females might incur different costs associated with darker stripes. This would allow reversal of signaling function. Green colouration could also serve as a cue for female provisioning quality as indicated by the strong correlation between colouration and chick body mass. Breeding house martins caught in Algeria suffer greater haemosporidian infection than European populations (Chapter 6). Similar parasite communities in European and North-African populations suggest transmission of parasites may occur during southward migration. Similarly to what was observed in great tits in Chapter 2 and 3, no relationship was found between parasite co-infection and Swiss house martin body condition. This thesis demonstrates that host-parasite and inter-parasite antagonistic interac¬tions exist in great tit populations. How these interactions play out is species dependent and varies geographically. I have demonstrated that interactions do not always follow the theory, as co-infection - which under the concept of virulence should increase parasitaemia and decrease body condition - showed no negative impact on great tit populations. We can now concentrate our efforts on characterising these antagonistic interactions, and with the advance in molecular methods, track and investigate how these interactions play out and what the effect on host fitness is.

IL-17F co-expression improves cell growth characteristics and enhances recombinant protein production during CHO cell line engineering.

The generation of a high productivity cell line is a critical step in the production of a therapeutic protein. Many innovative engineering strategies have been devised in order to maximize the expression rate of production cells for increased process efficiency. Less effort has focused on improvements to the cell line generation process, which is typically long and laborious when using mammalian cells. Based on unexpected findings when generating stable CHO cell lines expressing human IL-17F, we studied the benefit of expressing this protein during the establishment of production cell lines. We demonstrate that IL-17F expression enhances the rate of selection and overall number of selected cell lines as well as their transgene expression levels. We also show that this benefit is observed with different parental CHO cell lines and selection systems. Furthermore, IL-17F expression improves the efficiency of cell line subcloning processes. IL-17F can therefore be exploited in a standard manufacturing process to obtain higher productivity clones in a reduced time frame.

Measurements of glial metabolic fluxes with C-11-acetate using positron emission and an adapted NMR-based metabolic modeling approach

Objectives: Acetate brain metabolism has the particularity to occur specifically in glial cells. Labeling studies, using acetate labeled either with 13C (NMR) or 11C (PET), are governed by the same biochemical reactions and thus follow the same mathematical principles. In this study, the objective was to adapt an NMR acetate brain metabolism model to analyse [1-11C]acetate infusion in rats. Methods: Brain acetate infusion experiments were modeled using a two-compartment model approach used in NMR.1-3 The [1-11C]acetate labeling study was done using a beta scintillator.4 The measured radioactive signal represents the time evolution of the sum of all labeled metabolites in the brain. Using a coincidence counter in parallel, an arterial input curve was measured. The 11C at position C-1 of acetate is metabolized in the first turn of the TCA cycle to the position 5 of glutamate (Figure 1A). Through the neurotransmission process, it is further transported to the position 5 of glutamine and the position 5 of neuronal glutamate. After the second turn of the TCA cycle, tracer from [1-11C]acetate (and also a part from glial [5-11C]glutamate) is transferred to glial [1-11C]glutamate and further to [1-11C]glutamine and neuronal glutamate through the neurotransmission cycle. Brain poster session: oxidative mechanisms S460 Journal of Cerebral Blood Flow & Metabolism (2009) 29, S455-S466 Results: The standard acetate two-pool PET model describes the system by a plasma pool and a tissue pool linked by rate constants. Experimental data are not fully described with only one tissue compartment (Figure 1B). The modified NMR model was fitted successfully to tissue time-activity curves from 6 single animals, by varying the glial mitochondrial fluxes and the neurotransmission flux Vnt. A glial composite rate constant Kgtg=Vgtg/[Ace]plasma was extracted. Considering an average acetate concentration in plasma of 1 mmol/g5 and the negligible additional amount injected, we found an average Vgtg = 0.08±0.02 (n = 6), in agreement with previous NMR measurements.1 The tissue time-activity curve is dominated by glial glutamate and later by glutamine (Figure 1B). Labeling of neuronal pools has a low influence, at least for the 20 mins of beta-probe acquisition. Based on the high diffusivity of CO2 across the blood-brain barrier; 11CO2 is not predominant in the total tissue curve, even if the brain CO2 pool is big compared with other metabolites, due to its strong dilution through unlabeled CO2 from neuronal metabolism and diffusion from plasma. Conclusion: The two-compartment model presented here is also able to fit data of positron emission experiments and to extract specific glial metabolic fluxes. 11C-labeled acetate presents an alternative for faster measurements of glial oxidative metabolism compared to NMR, potentially applicable to human PET imaging. However, to quantify the relative value of the TCA cycle flux compared to the transmitochondrial flux, the chemical sensitivity of NMR is required. PET and NMR are thus complementary.

Regulierungen an der Schnittstelle zwischen den Ressourcen Wald und Klima : Einflussfaktoren auf die Inwertsetzung der CO₂-Senkenleistung des Waldes

Les forêts dont le volume sur pied augmente contribuent à atténuer les changements climatiques et constituent un puits de carbone. En Suisse, seul très peu d'entreprises forestières valorisent le service de puits de carbone. Ce travail vise à chercher les raisons expliquant cette réticence. Les facteurs politiques et juridiques influençant les décisions des entreprises forestières sont analysées à l'aide du modèle des régimes institutionnels de ressource. Les résultats obtenus sont vérifiés et complétés à l'aide d'informations collectées lors d'interviews d'experts menées auprès d'entreprises forestières et décideurs politiques. Cette étude identifie des facteurs favorisant ou entravant la valorisation du service de puits de carbone des forêts et propose des options d'action.

The neurochemical profile quantified by in vivo 1H NMR spectroscopy.

Proton NMR spectroscopy is emerging from translational and preclinical neuroscience research as an important tool for evidence based diagnosis and therapy monitoring. It provides biomarkers that offer fingerprints of neurological disorders even in cases where a lesion is not yet observed in MR images. The collection of molecules used as cerebral biomarkers that are detectable by (1)H NMR spectroscopy define the so-called "neurochemical profile". The non-invasive quality of this technique makes it suitable not only for diagnostic purposes but also for therapy monitoring paralleling an eventual neuroprotection. The application of (1)H NMR spectroscopy in basic and translational neuroscience research is discussed here.

Prospective and retrospective motion correction in diffusion magnetic resonance imaging of the human brain.

Diffusion-weighting in magnetic resonance imaging (MRI) increases the sensitivity to molecular Brownian motion, providing insight in the micro-environment of the underlying tissue types and structures. At the same time, the diffusion weighting renders the scans sensitive to other motion, including bulk patient motion. Typically, several image volumes are needed to extract diffusion information, inducing also inter-volume motion susceptibility. Bulk motion is more likely during long acquisitions, as they appear in diffusion tensor, diffusion spectrum and q-ball imaging. Image registration methods are successfully used to correct for bulk motion in other MRI time series, but their performance in diffusion-weighted MRI is limited since diffusion weighting introduces strong signal and contrast changes between serial image volumes. In this work, we combine the capability of free induction decay (FID) navigators, providing information on object motion, with image registration methodology to prospectively--or optionally retrospectively--correct for motion in diffusion imaging of the human brain. Eight healthy subjects were instructed to perform small-scale voluntary head motion during clinical diffusion tensor imaging acquisitions. The implemented motion detection based on FID navigator signals is processed in real-time and provided an excellent detection performance of voluntary motion patterns even at a sub-millimetre scale (sensitivity≥92%, specificity>98%). Motion detection triggered an additional image volume acquisition with b=0 s/mm2 which was subsequently co-registered to a reference volume. In the prospective correction scenario, the calculated motion-parameters were applied to perform a real-time update of the gradient coordinate system to correct for the head movement. Quantitative analysis revealed that the motion correction implementation is capable to correct head motion in diffusion-weighted MRI to a level comparable to scans without voluntary head motion. The results indicate the potential of this method to improve image quality in diffusion-weighted MRI, a concept that can also be applied when highest diffusion weightings are performed.

The co-evolution of social institutions, demography, and large-scale human cooperation.

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small- to large-scale societies involves understanding how these institutions co-evolve with demography. We study this using a demographically explicit model of institution formation in a patch-structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co-evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small- to large-scale social groups.

Prevalence and risk of Down syndrome in monozygotic and dizygotic multiple pregnancies in Europe: implications for prenatal screening.

OBJECTIVE: To determine risk of Down syndrome (DS) in multiple relative to singleton pregnancies, and compare prenatal diagnosis rates and pregnancy outcome. DESIGN: Population-based prevalence study based on EUROCAT congenital anomaly registries. SETTING: Eight European countries. POPULATION: 14.8 million births 1990-2009; 2.89% multiple births. METHODS: DS cases included livebirths, fetal deaths from 20 weeks, and terminations of pregnancy for fetal anomaly (TOPFA). Zygosity is inferred from like/unlike sex for birth denominators, and from concordance for DS cases. MAIN OUTCOME MEASURES: Relative risk (RR) of DS per fetus/baby from multiple versus singleton pregnancies and per pregnancy in monozygotic/dizygotic versus singleton pregnancies. Proportion of prenatally diagnosed and pregnancy outcome. STATISTICAL ANALYSIS: Poisson and logistic regression stratified for maternal age, country and time. RESULTS: Overall, the adjusted (adj) RR of DS for fetus/babies from multiple versus singleton pregnancies was 0.58 (95% CI 0.53-0.62), similar for all maternal ages except for mothers over 44, for whom it was considerably lower. In 8.7% of twin pairs affected by DS, both co-twins were diagnosed with the condition. The adjRR of DS for monozygotic versus singleton pregnancies was 0.34 (95% CI 0.25-0.44) and for dizygotic versus singleton pregnancies 1.34 (95% CI 1.23-1.46). DS fetuses from multiple births were less likely to be prenatally diagnosed than singletons (adjOR 0.62 [95% CI 0.50-0.78]) and following diagnosis less likely to be TOPFA (adjOR 0.40 [95% CI 0.27-0.59]). CONCLUSIONS: The risk of DS per fetus/baby is lower in multiple than singleton pregnancies. These estimates can be used for genetic counselling and prenatal screening.

The co-evolution of culturally inherited altruistic helping and cultural transmission under random group formation.

Limited migration results in kin selective pressure on helping behaviors under a wide range of ecological, demographic and life-history situations. However, such genetically determined altruistic helping can evolve only when migration is not too strong and group size is not too large. Cultural inheritance of helping behaviors may allow altruistic helping to evolve in groups of larger size because cultural transmission has the potential to markedly decrease the variance within groups and augment the variance between groups. Here, we study the co-evolution of culturally inherited altruistic helping behaviors and two alternative cultural transmission rules for such behaviors. We find that conformist transmission, where individuals within groups tend to copy prevalent cultural variants (e.g., beliefs or values), has a strong adverse effect on the evolution of culturally inherited helping traits. This finding is at variance with the commonly held view that conformist transmission is a crucial factor favoring the evolution of altruistic helping in humans. By contrast, we find that under one-to-many transmission, where individuals within groups tend to copy a "leader" (or teacher), altruistic helping can evolve in groups of any size, although the cultural transmission rule itself hitchhikes rather weakly with a selected helping trait. Our results suggest that culturally determined helping behaviors are more likely to be driven by "leaders" than by popularity, but the emergence and stability of the cultural transmission rules themselves should be driven by some extrinsic factors.

In vivo 13C NMR spectroscopy and metabolic modeling in the brain: a practical perspective.

In vivo 13C NMR spectroscopy has the unique capability to measure metabolic fluxes noninvasively in the brain. Quantitative measurements of metabolic fluxes require analysis of the 13C labeling time courses obtained experimentally with a metabolic model. The present work reviews the ingredients necessary for a dynamic metabolic modeling study, with particular emphasis on practical issues.

Proton NMR of (15)N-choline metabolites enhanced by dynamic nuclear polarization.

Chemical shifts of protons can report on metabolic transformations such as the conversion of choline to phosphocholine. To follow such processes in vivo, magnetization can be enhanced by dynamic nuclear polarization (DNP). We have hyperpolarized in this manner nitrogen-15 spins in (15)N-labeled choline up to 3.3% by irradiating the 94 GHz electron spin resonance of admixed TEMPO nitroxide radicals in a magnetic field of 3.35 T during ca. 3 h at 1.2 K. The sample was subsequently transferred to a high-resolution magnet, and the enhanced polarization was converted from (15)N to methyl- and methylene protons, using the small (2,3)J((1)H,(15)N) couplings in choline. The room-temperature lifetime of nitrogen polarization in choline, T(1)((15)N) approximately 200 s, could be considerably increased by partial deuteration of the molecule. This procedure enables studies of choline metabolites in vitro and in vivo using DNP-enhanced proton NMR.