Population genetics of Capercaillie (Tetrao urogallus) in the Jura and the Pyrenees: a non-invasive approach to avian conservation genetics

RÉSUMÉ Le Grand tétras est un galliforme de montagne apparenté au faisan et au tétras lyre. Il est distribué de manière continue à travers la toundra et les montagnes de moyenne altitude en Europe de l'ouest. Toutefois, les populations d'Europe de l'ouest ont subi un déclin constant au cours des derniers siècles. Les causes de ce déclin sont probablement liées à l'activité humaine, telle .que l'élevage ou le tourisme, qui ont engendré une modification et une fragmentation de l'habitat de l'espèce. Malheureusement, les populations soumises à de forts déclins démographiques peuvent subir des effets génétiques (augmentation de la consanguinité et perte de diversité génétique) pouvant diminuer leur potentiel de reproduction et conduire irrémédiablement à l'extinction. Cette thèse présente les analyses conduites dans le but d'estimer l'impact du déclin démographique des populations de Grand tétras sur l'étendue et la distribution de leur variabilité génétique dans le Jura et dans les Pyrénées. Du fait de la législation locale protégeant les tétraonidés en général, mais également en raison de la biologie très cryptique du Grand tétras, l'ensemble des analyses de cette étude a été réalisé à partir de matériel génétique extrait des fientes (ou échantillonnage génétique non invasif). Dans la première partie de l'étude, je détaille les protocoles d'extraction. d'ADN et d'amplification par PCR modifiés à partir des protocoles classiques utilisant des échantillons conventionnels, riches en ADN. L'utilisation d'ADN fécal impose des contraintes dues à la mauvaise qualité et à la faible quantité du matériel génétique à disposition dans les fientes. Ces contraintes ont pu être partiellement contournées en réalisant des répétitions multiples du génotypage afin d'obtenir un degré de fiabilité suffisante. J'ai également analysé les causes de la dégradation de l'ADN dans les excréments. Parmi les causes les plus communes, telles que l'activité bactérienne, l'hydrolyse spontanée et la dégradation enzymatique par les DNases libres, c'est ce dernier facteur qui apparaît comme étant la cause majeure et la plus rapide responsable de la dégradation de la qualité des échantillons. La rapidité de l'action enzymatique suggère que les plans d'échantillonnages de excréments sur le terrain pourraient être optimisés en les réalisant dans des conditions climatiques froides et sèches, favorisant ainsi l'inhibition des DNases. La seconde partie de la thèse est une étude par simulation visant à déterminer la capacité du logiciel Structure à identifier les structures génétiques complexes et hiérarchiques fréquemment rencontrées dans les populations naturelles, et ce en utilisant différents types de marqueurs génétiques. Les troisième et quatrième parties de cette thèse décrivent le statut génétique des populations résiduelles du Jura et des Pyrénées à partir de l'analyse de 11 loci microsatellites. Nous n'avons pas pu mettre en évidence dans les deux populations des effets liés à la consanguinité ou à la réduction de la diversité génétique. De plus, la différenciation génétique entre les patches d'habitats favorables reste modérée et corrélée à la distance géographique, ce qui suggère que la dispersion d'individus entre les patches a été importante au moins pendant ces dernières générations. La comparaison des paramètres de la diversité génétique avec ceux d'autres populations de Grand tétras, ou d'autres espèces proches, indique que la population du Jura a retenu une proportion importante de sa diversité originelle. Ces résultats suggèrent que le déclin récent des populations a jusqu'ici eu un impact modéré sur les facteurs génétiques et que ces populations semblent avoir conservé le potentiel génétique nécessaire à leur survie à long terme. Finalement, en cinquième partie, l'analyse de l'apparentement entre les mâles qui participent à la parade sur les places de chant (leks) indique que ces derniers sont distribués en agrégats de manière non aléatoire, préférentiellement entre individus apparentés. De plus, la corrélation entre les distances génétique et géographique entre les leks est en accord avec les motifs d'isolement par la distance mis en évidence à d'autres niveaux hiérarchiques (entre patches d'habitat et populations), ainsi qu'avec les études menées sur d'autres espèces ayant choisi ce même système de reproduction. En conclusion, cette première étude basée uniquement sur de l'ADN nucléaire aviaire extrait à partir de fèces a fourni des informations nouvelles qui n'auraient pas pu être obtenues par une méthode d'observation sur le terrain ou d'échantillonnage génétique classique. Aucun oiseau n'a été dérangé ou capturé, et les résultats sont comparables à d'autres études concernant des espèces proches. Néanmoins, la taille de ces populations approche des niveaux au-dessous desquels la survie à long terme est fortement incertaine. La persistance de la diversité génétique pour les prochaines générations reste en conséquence liée à la survie des adultes et à une reprise du succès de la reproduction. ABSTRACT Capercaillie (Tetrao urogallus) is a large grouse that is continuously distributed across the tundra and the mid-high mountains of Western Europe. However, the populations in Western Europe have been showing a constant decline during the last decades. The causes for this decline are possibly related to human activities, such as cattle breeding and tourism that have both led to habitat modification and fragmentation. Unfortunately, populations that have undergone drastic demographic bottlenecks often go through genetic processes of inbreeding and loss of diversity that decrease their fitness and eventually lead to extinction. This thesis presents the investigations conducted to estimate the impact of the demographic decline of capercaillie populations on the extent and distribution of their genetic variability in the Jura and in the Pyrenees mountains. Because grouse are protected by wildlife legislation, and also because of the cryptic behaviour of capercaillie, all DNA material used in this study was extracted from faeces (non-invasive genetic sampling). In the first part of my thesis, I detail the protocols of DNA extraction and PCR amplification adapted from classical methods using conventional DNA-rich samples. The use of faecal DNA imposes specific constraints due to the low quantity and the highly degraded genetic material available. These constraints are partially overcome by performing multiple genotyping repetitions to obtain sufficient reliability. I also investigate the causes of DNA degradation in faeces. Among the main degraders, namely bacterial activity, spontaneous hydrolysis, and free-¬DNase activities, the latter was pointed out as the most important according to our experiments. These enzymes degrade DNA very rapidly, and, as a consequence, faeces sampling schemes must be planned preferably in cold and dry weather conditions, allowing for enzyme activity inhibition. The second part of the thesis is a simulation study aiming to assess the capacity of the software Structure to detect population structure in hierarchical models relevant to situations encountered in wild populations, using several genetic markers. The methods implemented in Structure appear efficient in detecting the highest hierarchical structure. The third and fourth parts of the thesis describe the population genetics status of the remaining Jura and Pyrenees populations using 11 microsatellite loci. In either of these populations, no inbreeding nor reduced genetic diversity was detected. Furthermore, the genetic differentiation between patches defined by habitat suitability remains moderate and correlated with geographical distance, suggesting that significant dispersion between patches was at work at least until the last generations. The comparison of diversity indicators with other species or other populations of capercaillie indicate that population in the Jura has retained a large part of its original genetic diversity. These results suggest that the recent decline has had so forth a moderate impact on• genetic factors and that these populations might have retained the potential for long term survival, if the decline is stopped. Finally, in the fifth part, the analysis of relatedness between males participating in the reproduction parade, or lek, indicate that capercaillie males, like has been shown for some other grouse species, gather on leks• among individuals that are more related than the average of the population. This pattern appears to be due to both population structure and kin-association. As a conclusion, this first study relying exclusively on nuclear DNA extracted from faeces has provided novel information that was not available through field observation or classical genetic sampling. No bird has been captured or disturbed, and the results are consistent with other studies of closely related species. However, the size of these populations is approaching thresholds below which long-term survival is unlikely. The persistence of genetic diversity for the forthcoming generations remains therefore bond to adult survival and to the increase of reproduction success.

The Influence of Process Conditions on the Deresination Efficiency in Mechanical Pulp Washing

The aim of this thesis was to produce information for the estimation of the flow balance of wood resin in mechanical pulping and to demonstrate the possibilities for improving the efficiency of deresination in practice. It was observed that chemical changes in wood resin take place only during peroxide bleaching, a significant amount of water dispersed wood resin is retained in the pulp mat during dewatering and the amount of wood resin in the solid phase of the process filtrates is very small. On the basis of this information there exist three parameters related to behaviour of wood resin that determine the flow balance in the process: 1. The liberation of wood resin to the pulp water phase 2. Theretention of water dispersed wood resin in dewatering 3. The proportion of wood resin degraded in the peroxide bleaching The effect of different factors on these parameters was evaluated with the help of laboratory studies and a literature survey. Also, information related to the values of these parameters in existing processes was obtained in mill measurements. With the help of this information, it was possible to evaluate the deresination efficiency and the effect of different factors on this efficiency in a pulping plant that produced low-freeness mechanical pulp. This evaluation showed that the wood resin content of mechanical pulp can be significantly decreased if there exists, in the process, a peroxide bleaching and subsequent washing stage. In the case of an optimal process configuration, as high as a 85 percent deresination efficiency seems to be possible with a water usage level of 8 m3/o.d.t.

Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits

BACKGROUND: Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance. RESULTS: Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group. CONCLUSION: Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to to elucidate the effects of lipid deposition on muscle metabolism in pigs.

Genome-wide transcriptional responses to shade: Linking shade avoidance and auxin

Plants have the ability to use the composition of incident light as a cue to adapt development and growth to their environment. Arabidopsis thaliana as well as many crops are best adapted to sunny habitats. When subjected to shade, these plants exhibit a variety of physiological responses collectively called shade avoidance syndrome (SAS). It includes increased growth of hypocotyl and petioles, decreased growth rate of cotyledons and reduced branching and crop yield. These responses are mainly mediated by phytochrome photoreceptors, which exist either in an active, far-red light (FR) absorbing or an inactive, red light (R) absorbing isoform. In direct sunlight, the R to FR light (R/FR) ratio is high and converts the phytochromes into their physiologically active state. The phytochromes interact with downstream transcription factors such as PHYTOCHROME INTERACTING FACTOR (PIF), which are subsequently degraded. Light filtered through a canopy is strongly depleted in R, which result in a low R/FR ratio and renders the phytochromes inactive. Protein levels of downstream transcription factors are stabilized, which initiates the expression of shade-induced genes such as HFR1, PIL1 or ATHB-2. In my thesis, I investigated transcriptional responses mediated by the SAS in whole Arabidopsis seedlings. Using microarray and chromatin immunoprecipitation data, we identified genome-wide PIF4 and PIF5 dependent shade regulated gene as well as putative direct target genes of PIF5. This revealed evidence for a direct regulatory link between phytochrome signaling and the growth promoting phytohormone auxin (IAA) at the level of biosynthesis, transport and signaling. Subsequently, it was shown, that free-IAA levels are upregulated in response to shade. It is assumed that shade-induced auxin production takes predominantly place in cotyledons of seedlings. This implies, that IAA is subsequently transported basipetally to the hypocotyl and enhances elongation growth. The importance of auxin transport for growth responses has been established by chemical and genetic approaches. To gain a better understanding of spatio-temporal transcriptional regulation of shade-induce auxin, I generated in a second project, an organ specific high throughput data focusing on cotyledon and hypocotyl of young Arabidopsis seedlings. Interestingly, both organs show an opposite growth regulation by shade. I first investigated the spatio-transcriptional regulation of auxin re- sponsive gene, in order to determine how broad gene expression pattern can be explained by the hypothesized movement of auxin from cotyledons to hypocotyls in shade. The analysis suggests, that several genes are indeed regulated according to our prediction and others are regulated in a more complex manner. In addition, analysis of gene families of auxin biosynthetic and transport components, lead to the identification of essential family members for shade-induced growth re- sponses, which were subsequently experimentally confirmed. Finally, the analysis of expression pattern identified several candidate genes, which possibly explain aspects of the opposite growth response of the different organs.

A formin-nucleated actin aster concentrates cell wall hydrolases for cell fusion in fission yeast.

Cell-cell fusion is essential for fertilization. For fusion of walled cells, the cell wall must be degraded at a precise location but maintained in surrounding regions to protect against lysis. In fission yeast cells, the formin Fus1, which nucleates linear actin filaments, is essential for this process. In this paper, we show that this formin organizes a specific actin structure-the actin fusion focus. Structured illumination microscopy and live-cell imaging of Fus1, actin, and type V myosins revealed an aster of actin filaments whose barbed ends are focalized near the plasma membrane. Focalization requires Fus1 and type V myosins and happens asynchronously always in the M cell first. Type V myosins are essential for fusion and concentrate cell wall hydrolases, but not cell wall synthases, at the fusion focus. Thus, the fusion focus focalizes cell wall dissolution within a broader cell wall synthesis zone to shift from cell growth to cell fusion.

Anaerobic treatment of deinking pulp plant effluents

Anaerobic treatment as a first biological stage in wastewater treatment is nowadays a well-established technology in recycled paper processing mills using closed water circuits. Today further developed high-rate processes and especially high-tower reactors are also able to handle lower organic loads and become therefore feasible for deinking pulp plant effluents. The interest in the anaerobic method is based on a positive energy balance in form of biogas production and low biomass yield from the process. The anaerobic treatment method was researched and its suitability for the deinking pulp plant effluents was tested experimentally at Stora Enso Maxau mill. In the theory, the deinking pulp process is introduced and the effluents from the deinking process are characterized. The anaerobic treatment is brought up in depth in terms of its use for the deinking effluents, and different kind of reactor types are presented. In addition, other wastewater treatment methods are shortly introduced with the focus on tertiary treatment. Static biodegradability tests were carried out for the wastewaters both anaerobically and aerobically. Based on the results, the deinking effluents can be degraded anaerobically, and inhibition to the methanogenic bacteria was not noticed. In the aerobic static test a good performance of the existing wastewater treatment plant at Maxau mill was proved. Later on pilot trials with sequential anaerobic-aerobic treatment were carried out for the deinking effluents. The anaerobic reactor used was a so called internal circulation reactor. The results confirmed that the combination of the anaerobic treatment and the aerobic activated sludge process is a suitable method for deinking wastewaters with a COD reduction as good as with a two stage aerobic method. When combined with the outstanding quality of the produced biogas and the cost savings acquired from the lower sludge production, the anaerobic treatment was found to be an especially favorable treatment method.

Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs.

Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the other proteins. Yet unexplained, the increased levels of HSP messenger RNAs (mRNAs) may exceed 100 times the ensuing relative levels of HSP proteins. We used here high-throughput quantitative proteomics and targeted mRNA quantification to estimate in human cell cultures the mass and copy numbers of the most abundant proteins that become significantly accumulated, depleted, or unchanged during and following 4 h at 41 °C, which we define as mild heat shock. This treatment caused a minor across-the-board mass loss in many housekeeping proteins, which was matched by a mass gain in a few HSPs, predominantly cytosolic HSPCs (HSP90s) and HSPA8 (HSC70). As the mRNAs of the heat-depleted proteins were not significantly degraded and less ribosomes were recruited by excess new HSP mRNAs, the mild depletion of the many housekeeping proteins during heat shock was attributed to their slower replenishment. This differential protein expression pattern was reproduced by isothermal treatments with Hsp90 inhibitors. Unexpectedly, heat-treated cells accumulated 55 times more new molecules of HSPA8 (HSC70) than of the acknowledged heat-inducible isoform HSPA1A (HSP70), implying that when expressed as net copy number differences, rather than as mere "fold change" ratios, new biologically relevant information can be extracted from quantitative proteomic data. Raw data are available via ProteomeXchange with identifier PXD001666.

Compositional influence on the electrical performance of zinc indium tin oxide transparent thin-film transistors

In this work, zinc indium tin oxide layers with different compositions are used as the active layer of thin film transistors. This multicomponent transparent conductive oxide is gaining great interest due to its reduced content of the scarce indium element. Experimental data indicate that the incorporation of zinc promotes the creation of oxygen vacancies. In thin-film transistors this effect leads to a higher threshold voltage values. The field-effect mobility is also strongly degraded, probably due to coulomb scattering by ionized defects. A post deposition annealing in air reduces the density of oxygen vacancies and improves the fieldeffect mobility by orders of magnitude. Finally, the electrical characteristics of the fabricated thin-film transistors have been analyzed to estimate the density of states in the gap of the active layers. These measurements reveal a clear peak located at 0.3 eV from the conduction band edge that could be attributed to oxygen vacancies.

Alternatively spliced proline-rich cassettes link WNK1 to aldosterone action.

The thiazide-sensitive NaCl cotransporter (NCC) is important for renal salt handling and blood-pressure homeostasis. The canonical NCC-activating pathway consists of With-No-Lysine (WNK) kinases and their downstream effector kinases SPAK and OSR1, which phosphorylate NCC directly. The upstream mechanisms that connect physiological stimuli to this system remain obscure. Here, we have shown that aldosterone activates SPAK/OSR1 via WNK1. We identified 2 alternatively spliced exons embedded within a proline-rich region of WNK1 that contain PY motifs, which bind the E3 ubiquitin ligase NEDD4-2. PY motif-containing WNK1 isoforms were expressed in human kidney, and these isoforms were efficiently degraded by the ubiquitin proteasome system, an effect reversed by the aldosterone-induced kinase SGK1. In gene-edited cells, WNK1 deficiency negated regulatory effects of NEDD4-2 and SGK1 on NCC, suggesting that WNK1 mediates aldosterone-dependent activity of the WNK/SPAK/OSR1 pathway. Aldosterone infusion increased proline-rich WNK1 isoform abundance in WT mice but did not alter WNK1 abundance in hypertensive Nedd4-2 KO mice, which exhibit high baseline WNK1 and SPAK/OSR1 activity toward NCC. Conversely, hypotensive Sgk1 KO mice exhibited low WNK1 expression and activity. Together, our findings indicate that the proline-rich exons are modular cassettes that convert WNK1 into a NEDD4-2 substrate, thereby linking aldosterone and other NEDD4-2-suppressing antinatriuretic hormones to NCC phosphorylation status.

Neurofilament proteins in the postnatal rat hippocampus. Developmental expression and changes in experimental epilepsy

Neurofilament proteins (NFs) are the major components of the intermediate filaments of the neuronal cytoskeleton. The three different NF proteins; the low (NF-L), medium (NF-M),and dendrites.NF proteins play an important role in neuronal development, and plasticity,and seem to contribute to the pathophysiology of several diseases. However, the detailed expression patterns of NF proteins in the course of postnatal aturation, and in response to seizures in the rat have remained unknown. In this work, I have studied the developmental expression and cellular distribution of the three NF proteins in the rat hippocampus during the postnatal development. The reactivity of NF proteins in response to kainic acid (KA)-induced status epilepticus (SE)was studied in the hippocampus of 9-day-old rats, and using in vitro organotypic hippocampal slices cultures prepared from P6-7 rats. The results showed that NF-L and NF-M proteins are expressed already at the postnatal day 1, while the expression of NF-H mainly occurred during the second postnatal week. The immunoreactivity of NF proteins varied depending on the cell type and sub-cellular location in the hippocampus. In adult rats, KA-induced SE typically results in severe and permanent NF degradation. However, in our P9 rats KA-induced SE resulted in a transient increase in the expression of NF proteins during the first few hours but not degradation. No neuronal death or mossy fiber sprouting was observed at any time after SE. The in vitro studies with OHCs, which mimick the in vivo developing models where a local injection of KA is applied(e.g. intrahippocampal), indicated that NF proteins were rapidly degraded in response to KA treatment, this effect being effectively inhibited by the treatment with the AMPA receptor antagonist CNQX, and calpain inhibitor MDL-28170. These compounds also significantly ameliorated the KA-induced region-specific neuronal damage. The NMDA receptor antagonist and the L-type Ca2+ channel blocker did not have any significant effect. In conclusion, the results indicate that the developmental expression of NF in the rat hippocampus is differentially regulated and targeted in the different hippocampal cell types during the postnatal development. Furthermore, despite SE, the mechanisms leading to NF degradation and neuronal death are not activated in P9 rats unlike in adults. The reason for this remains unknown. The results in organotypic hippocampal cultures confirm the validity of this in vitro model to study development processes, and to perform pharmacological studies. The results also suggest that calpain proteases as interesting pharmacological targets to reduce neuronal damage after acute excitotoxic insults.

Forest Transition in Madagascar's Highlands: Initial Evidence and Implications

Madagascar is renowned for the loss of the forested habitat of lemurs and other species endemic to the island. Less well known is that in the highlands, a region often described as an environmental "basket-case" of fire-degraded, eroded grasslands, woody cover has been increasing for decades. Using information derived from publically available high- and medium-resolution satellites, this study characterizes tree cover dynamics in the highlands of Madagascar over the past two decades. Our results reveal heterogeneous patterns of increased tree cover on smallholder farms and village lands, spurred by a mix of endogenous and exogenous forces. The new trees play important roles in rural livelihoods, providing renewable supplies of firewood, charcoal, timber and other products and services, as well as defensible claims to land tenure in the context of a decline in the use of hillside commons for grazing. This study documents this nascent forest transition through Land Change Science techniques, and provides a prologue to political ecological analysis by setting these changes in their social and environmental context and interrogating the costs and benefits of the shift in rural livelihood strategies.

Biokaasun syöttö maakasuverkostoon

Biokaasua syntyy mm. kaatopaikoilla, jätevedenpuhdistamoilla ja biokaasureaktoreissa, kun bakteerit hajottavat orgaanista ainesta hapettomissa olosuhteissa. Biokaasun tärkein ainesosa on metaani, jota biokaasussa on tyypillisesti hieman yli puolet. Muu osa biokaasusta on pääosin hiilidioksidia, mutta se sisältää myös paljon erilaisia epäpuhtauksia, jotka vaikeuttavat biokaasun hyötykäyttöä. Suomeen tuotava maakaasu puolestaan on lähes puhdasta metaania. Tämä diplomityö suoritettiin Gasum Oy:lle ja sen tarkoituksena oli tutkia millaisia toimenpiteitä vaaditaan, jotta biokaasua voidaan syöttää Suomen maakaasuverkostoon. Työssä suoritettiin katsaus biokaasun puhdistus- ja jalostusmenetelmiin, joilla biokaasun sisältämät epäpuhtaudet poistetaan ja metaanipitoisuus nostetaan lähes maakaasun tasolle hiilidioksidia poistamalla. Lisäksi työssä simuloitiin biokaasun syöttöä maakaasuverkostoon eri koostumuksin ja maakaasuverkoston eri osista näin syntyvän seoskaasun ominaisuuksien määrittämiseksi simulointiohjelma Simonen avulla. Työssä myös etsittiin parasta keinoa jäljittää maakaasuverkoston kaasun laatua ja hallita energiatasetta, kun kaasun laatu ei enää ole kaikkialla sama. Lisäksi suoritettiin lyhyt katsaus biokaasusyötön vaikutuksista päästökauppaan ja maakaasuverkoston järjestelmävastaavan tehtävään. Työssä tultiin siihen tulokseen, että biokaasun syöttö maakaasuverkostoon on mahdollista vain, kun biokaasu puhdistetaan ja jalostetaan. Tällöin biokaasun ja maakaasun seos täyttää maakaasuverkoston kaasulle asetetut laatukriteerit, vaikka yksin biokaasu ei sitä tee. Parhaaksi keinoksi hallita maakaasun ja biokaasun laatua todettiin kaasukromatografien käyttö.

Effects of heparin on the uptake of lipoprotein lipase in rat liver

BACKGROUND: Lipoprotein lipase (LPL) is anchored at the vascular endothelium through interaction with heparan sulfate. It is not known how this enzyme is turned over but it has been suggested that it is slowly released into blood and then taken up and degraded in the liver. Heparin releases the enzyme into the circulating blood. Several lines of evidence indicate that this leads to accelerated flux of LPL to the liver and a temporary depletion of the enzyme in peripheral tissues. RESULTS: Rat livers were found to contain substantial amounts of LPL, most of which was catalytically inactive. After injection of heparin, LPL mass in liver increased for at least an hour. LPL activity also increased, but not in proportion to mass, indicating that the lipase soon lost its activity after being bound/taken up in the liver. To further study the uptake, bovine LPL was labeled with 125I and injected. Already two min after injection about 33 % of the injected lipase was in the liver where it initially located along sinusoids. With time the immunostaining shifted to the hepatocytes, became granular and then faded, indicating internalization and degradation. When heparin was injected before the lipase, the initial immunostaining along sinusoids was weaker, whereas staining over Kupffer cells was enhanced. When the lipase was converted to inactive before injection, the fraction taken up in the liver increased and the lipase located mainly to the Kupffer cells. CONCLUSIONS: This study shows that there are heparin-insensitive binding sites for LPL on both hepatocytes and Kupffer cells. The latter may be the same sites as those that mediate uptake of inactive LPL. The results support the hypothesis that turnover of endothelial LPL occurs in part by transport to and degradation in the liver, and that this transport is accelerated after injection of heparin.

Characterization of a MAF1 knockout mouse model

L'ARN polymérase 3 transcrit un petit groupe de gènes fortement exprimés et impliqués dans plusieurs mécanismes moléculaires. Les ARNs de transfert ou ARNt représentent plus ou moins la moitié du transcriptome de l'ARN polymérase 3. Ils sont directement impliqués dans la traduction des protéines en agissant comme transporteurs d'acides aminés qui sont incorporés à la chaîne naissante de polypeptides. Chez des levures cultivées dans un milieu jusqu'à épuisement des nutriments, Maf1 réprime la transcription par l'ARN polymérase 3, favorisant ainsi l'économie énergétique cellulaire. Dans un modèle de cellules de mammifères, MAF1 réprime aussi la transcription de l'ARN polymérase 3 dans des conditions de stress, cependant il n'existe aucune donnée quant à son rôle chez un mammifère vivant. Pendant mon doctorat, j'ai utilisé une souris délétée pour le gène Maf1 afin de connaître les effets de ce gène chez un mammifère. Etonnamment, la souris Maf1-­‐/-­‐ est résistante à l'obésité même si celle-­‐ci est nourrie avec une nourriture riche en matières grasses. Des études moléculaires et de métabolomiques ont montré qu'il existe des cycles futiles de production et dégradation des lipides et des ARNt, ce qui entraîne une augmentation de la dépense énergique et favorise la résistance à l'obésité. En plus de la caractérisation de la souris Maf1-­‐/-­‐, pendant ma thèse j'ai également développé une méthode afin de normaliser les données de ChIP-­‐sequencing. Cette méthode est fondée sur l'utilisation d'un contrôle interne, représenté ici par l'ajout d'une quantité fixe de chromatine provenant d'un organisme différent de celui étudié. La méthode a amélioré considérablement la reproductibilité des valeurs entre réplicas biologiques. Elle a aussi révélé des différences entre échantillons issus de conditions différentes. Une occupation supérieure de l'ARN polymérase 3 sur les gènes Pol 3 chez les souris Maf1 KO entraîne une augmentation du niveau de précurseurs d'ARNt, ayant pour effet probable la saturation de la machinerie de maturation des ARNt. En effet, chez les souris Maf1 KO, le pourcentage d'ARNt modifiés est plus faible que chez les souris type sauvage. Ce déséquilibre entre le niveau de précurseurs et d'ARNt matures entraîne une diminution de la traduction protéique. Ces résultats ont permis d'identifier de nouvelles fonctions pour la protéine MAF1, comme étant une protéine régulatrice à la fois de la transcription mais aussi de la traduction et en étant un cible potentielle au traitement à l'obésité. -- RNA polymerase III (Pol 3) transcribes a small set of highly expressed genes involved in different molecular mechanisms. tRNAs account for almost half of the Pol 3 transcriptome and are involved in translation, bringing a new amino into the nascent polypeptide chain. In yeast, under nutrient deprivation, Maf1 acts for cell energetic economy by repressing Pol 3 transcription. In mammalian cells, MAF1 also represses Pol 3 activity under conditions of serum deprivation or DNA damages but nothing is known about its role in a mammalian organism. During my thesis studies, I used a Maf1 KO mouse model to characterize the effects of Maf1 deletion in a living animal. Surprisingly, the MAF1 KO mouse developed an unexpected phenotype, being resistant to high fat diet-­‐induced obesity and displaying an extended lifespan. Molecular and metabolomics characterizations revealed futile cycles of lipids and tRNAs, which are produced and immediately degraded, which increases energy consumption in the Maf1 KO mouse and probably explains in part the protection to obesity. Additionally to the mouse characterization, I also developed a method to normalize ChIP-­‐seq data, based on the addition of a foreign chromatin to be used as an internal control. The method improved reproducibility between replicates and revealed differences of Pol 3 occupancy between WT and Maf1 KO samples that were not seen without normalization to the internal control. I then established that increased Pol 3 occupancy in the Maf1 KO mouse liver was associated with increased levels of tRNA precursor but not of mature tRNAs, the effective molecules involved in translation. The overproduction of precursor tRNAs associated with the deletion of Maf1 apparently overwhelms the tRNA processing machinery as the Maf1 KO mice have lower levels of fully modified tRNAs. This maturation defect directly impacts on translation efficiency as polysomic fractions and newly synthetized protein levels were reduced in the liver of the Maf1 KO mouse. Altogether, these results indicate new functions for MAF1, a regulator of both transcription and translation as well as a potential target for obesity treatment.

Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online ( xcmsonline.scripps.edu ). The results showed that heating at an elevated temperature of 100 °C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250 °C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250 °C, 300s) with a significant formation of degradation and transformation products. The analysis of 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30 s). For example, tri- and diorganophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was identified in both the underivatized and derivatized forms of the plasma extracts and small molecule standard mixture, and was likely generated from oleic acid. Overall these analyses show that small molecules and metabolites undergo significant time-sensitive alterations when exposed to elevated temperatures, especially those conditions that mimic sample preparation and analysis in GC/MS experiments.