Mechanisms involved in the maintenance of inbreeding depression in gynodioecious "Silene vulgaris" (Caryophyllaceae): an experimental investigation

Summary Gynodioecy, the joint occurrence of females and hermaphrodites within natural populations, is a widely studied mating system ever since Darwin (1877). It is an exceptional mating system because continuous selection is necessary to maintain it. Since females only reproduce through ovules whereas hermaphrodites transmit genes through ovules and pollen, larger female fitness, in terms of seed output, is required to allow their maintenance. Two non-exclusive mechanisms can account for the maintenance of females. First, as females do not produce pollen they can reallocate their resources towards a higher ovule production. Second, hermaphrodites can self- and cross-fertilize whereas females are obligate outcrossers. Thus hermaphrodites should partly suffer from inbreeding depression (i.e.: the fitness decline of inbred relative to outbred individuals) and thereby produce less fit progeny than females. This thesis investigated the effects of self- and cross-fertilization of heimaphrodites over two consecutive generations. Inbreeding depression increased across the successive stages of the life- cycle (i.e.: from "seed traits" to "reproductive traits") displaying large inbreeding depression estimates (up to 0.76). This investigation not only detected large inbreeding depression estimates but also detected mechanisms involved in the maintenance of inbreeding depression. For instance cryptic self-incompatibility which is here a larger in vivo pollen performance of distant pollen compared to self-pollen; the expression of inbreeding depression especially in late life-cycle stages, and the appearance of females in the progeny of selfed hermaphrodites. The female biased sex ratio in the progeny of selfed hermaphrodites was a surprising result and could either come from the sex determining mechanisms (complex nucleo-cytoplasmic interaction(s)) and/or from inbreeding depression. Indeed, we not only got females and hermaphrodites but also partial male-sterile (PMS) individuals (i.e.: individuals with differing number of viable stamens). We detected that inbred pollen bearing plants (excluding females) have less viable stamens per flower than outbred plants. A positive correlation was detected between inbreeding depression for the number of viable stamens per flower and the difference in sex ratio between inbred and outbred individuals. A positive relationship was also detected between inbreeding depression for pollen viability and inbreeding depression for number of viable stamens per flower. Each correlation can either account for pleiotropic effects (a major gene acting on the two considered traits) or linkage disequilibrium between genes controlling each of the two related traits. If we hypothesize that these correlations are due to a major gene with pleiotropic effects, the positive relationship between inbreeding depression for number of viable stamens per flower and inbreeding depression for pollen viability showed that deleterious alleles present on a major gene coding for pollen production and viability depressed male fitness within inbred plants. The positive relationship between sex ratio difference between inbred and outbred individuals and inbreeding depression for number of viable stamens per flower indicates that (1) either number of viable stamens per flower is, in addition to inbreeding, also affected by the loci coding for sex determinism or, (2) the presence of females within the progeny of selfed hermaphrodites is a consequence of large inbreeding depression inhibiting pollen production, or (3) sex is here determined by a combination of loci coding for sex expression and inbreeding depression for male reproductive traits. In conclusion, Silene vulgaris has been shown to be a good model for understanding the evolution of mating systems that promote outbreeding. Résumé La gynodïoécie est définie comme étant la présence simultanée d'hermaphrodites et de femelles au sein de populations naturelles d'une même espèce. Ce système de reproduction a toujours fasciné le monde scientifique depuis Darwin, comme en témoigne ses écrits (1876, 1877) sur les systèmes de reproduction chez les plantes. Les femelles ne transmettent leurs gènes qu'à travers leurs ovules alors que les hermaphrodites transmettent leurs gènes à la fois par la voie mâle (le pollen) et la voie femelle (les ovules). La condition pour que la gynodïoécie se maintienne nécessite donc une fitness de la fonction femelle plus élevée chez les femelles que chez les hermaphrodites. Deux mécanismes mutuellement non exclusifs peuvent expliquer le maintien des femelles au sein de ces populations gynodioïques. D'une part, les femelles peuvent réallouer les ressources non utilisées pour la production de pollen et peuvent par conséquent produire plus d'ovules. D'autre part, la reproduction des femelles ne peut se faire que par allo-fécondation alors que les hermaphrodites, peuvent se reproduire à la fois par auto- et allo-fécondation. L'autofécondation s'accompagne en général d'une diminution de fitness de la descendance relativement à la progéniture issue d'allo-fécondation ; ce phénomène est connu sous le nom de dépression de consanguinité. Cette thèse avait pour but de mettre en évidence une éventuelle dépression de consanguinité chez Silene vulgaris, une espèce gynodioïque. Des hermaphrodites, issus de trois vallées alpines, ont été auto- et allo¬fécondés sur deux générations successives. La dépression de consanguinité pouvant s'exprimer à tous les stades de vie d'un individu, plusieurs traits de fitness, allant du nombre de graines par fruit à la production de gamètes ont été mesurés sur différents stades de vie successifs. L'estimation de la dépression de consanguinité totale atteignait des valeurs allant de 0.52 à 0.76 selon la vallée considérée, ce qui indiquerait que les hermaphrodites ont tout intérêt à limiter l'autofécondation et que les femelles ne devraient pas avoir de peine à subsister dans les vallées étudiées. Par la même occasion des mécanismes diminuant la purge potentielle du fardeau génétique, et permettant ainsi le maintien du « niveau » de dépression de consanguinité et par conséquence le maintien de la gynodïoécie ont été mis en évidence. En effet, nos résultats montrent que la dépression de consanguinité s'exprimait tard dans le cycle de vie permettant ainsi à un certain nombre individus consanguins de transmettre leurs allèles délétères à la génération suivante. D'autre part, la croissance in vivo des tubes polliniques d'auto-pollen était plus lente que celle de l'allo-pollen et donc en situation de compétition directe, les ovules devraient plutôt être issus d'allo-fécondation, diminuant ainsi les chances de purges d'allèles délétères. Enfin, l'apparition de femelles dans la progéniture d'hermaphrodites autofécondés diminue aussi les chances de purge d'allèles délétères. Il nous a été impossible de déterminer si l'apparition de femelles dans la descendance d'hermaphrodites autofécondés était due au déterminisme génétique du sexe ou si la différence de sexe ratio entre la descendance auto- et allo-fécondée était due à une éventuelle dépression de consanguinité inhibant la production de pollen. Nous avons observé que S. vulgaris ne présentaient pas uniquement des hermaphrodites et des femelles mais aussi toute sorte d'individus intermédiaires avec un nombre variable d'étamines viables. Nous avons pu mettre' en évidence des corrélations positives entre (1) la différence de sexe ratio (la proportion d'individus produisant du pollen) entre individus consanguins et non consanguins et une estimation de la dépression de consanguinité pour le nombre d'étamines viables d'individus produisant du pollen, ainsi qu'entre (2) la dépression de consanguinité pour le nombre d'étamines viables et celle estimée pour la viabilité du pollen. Chaque corrélation indique soit l'effet d'un (ou plusieurs) gène(s) pléiotropique(s), soit un déséquilibre de liaison entre les gènes. En considérant que ces corrélations sont le résultat d'effet pléiotropiques, la relation entre le nombre d'étamines viables par fleur et la viabilité du pollen, indiquerait un effet négatif de la consanguinité sur la production et la viabilité du pollen due partiellement à un gène majeur. La seconde corrélation indiquerait soit que les gènes responsables de la détermination du sexe agissent aussi sur l'expression de la fonction mâle soit que l'expression du sexe est sujette à la dépression de consanguinité, ou encore un mélange des deux. Aux regards de ces résultats, Silene vulgaris s'est avéré être un bon modèle de compréhension de l'évolution des systèmes de reproduction vers la séparation des sexes.

Structural organization of alpha-subunit from purified and microsomal toad kidney (Na+ + K+)-ATPase as assessed by controlled trypsinolysis

The membrane organization of the alpha-subunit of purified (Na+ + K+)-ATPase ((Na+ + K+)-dependent adenosine triphosphate phosphorylase, EC 3.6.1.3) and of the microsomal enzyme of the kidney of the toad Bufo marinus was compared by using controlled trypsinolysis. With both enzyme preparations, digestions performed in the presence of Na+ yielded a 73 kDa fragment and in the presence of K+ a 56 kDa, a 40 kDa and small amounts of a 83 kDa fragment from the 96 kDa alpha-subunit. In contrast to mammalian preparations (Jørgensen, P.L. (1975) Biochim. Biophys. Acta 401, 399-415), trypsinolysis of the purified amphibian enzyme led to a biphasic loss of (Na+ + K+)-ATPase activity in the presence of both Na+ and K+. These data could be correlated with an early rapid cleavage of 3 kDa from the alpha-subunit in both ionic conditions and a slower degradation of the remaining 93 kDa polypeptide. On the other hand, in the microsomal enzyme, a 3 kDa shift of the alpha-subunit could only be produced in the presence of Na+. Our data indicate that (1) purification of the amphibian enzyme with detergent does not influence the overall topology of the alpha-subunit but produces a distinct structural alteration of its N-terminus and (2) the amphibian kidney enzyme responds to cations with similar conformational transitions as the mammalian kidney enzyme. In addition, anti alpha-serum used on digested enzyme samples revealed on immunoblots that the 40 kDa fragment was better recognized than the 56 kDa fragment. It is concluded that the NH2-terminal of the alpha-subunit contains more antigenic sites than the COOH-terminal domain in agreement with the results of Farley et al. (Farley, R.A., Ochoa, G.T. and Kudrow, A. (1986) Am. J. Physiol. 250, C896-C906).

Maintenance of male sterile germplasm in Brassica rapa in vitro propagation

Selostus: Isästeriilin kevätrypsin geeniaineksen ylläpito in vitro mikroviljelyllä

Social network architecture and the maintenance of deleterious cultural traits.

How have changes in communications technology affected the way that misinformation spreads through a population and persists? To what extent do differences in the architecture of social networks affect the spread of misinformation, relative to the rates and rules by which individuals transmit or eliminate different pieces of information (cultural traits)? Here, we use analytical models and individual-based simulations to study how a 'cultural load' of misinformation can be maintained in a population under a balance between social transmission and selective elimination of cultural traits with low intrinsic value. While considerable research has explored how network architecture affects percolation processes, we find that the relative rates at which individuals transmit or eliminate traits can have much more profound impacts on the cultural load than differences in network architecture. In particular, the cultural load is insensitive to correlations between an individual's network degree and rate of elimination when these quantities vary among individuals. Taken together, these results suggest that changes in communications technology may have influenced cultural evolution more strongly through changes in the amount of information flow, rather than the details of who is connected to whom.

Structural assessment of single amino acid mutations: application to TP53 function.

Single amino acid substitution is the type of protein alteration most related to human diseases. Current studies seek primarily to distinguish neutral mutations from harmful ones. Very few methods offer an explanation of the final prediction result in terms of the probable structural or functional effect on the protein. In this study, we describe the use of three novel parameters to identify experimentally-verified critical residues of the TP53 protein (p53). The first two parameters make use of a surface clustering method to calculate the protein surface area of highly conserved regions or regions with high nonlocal atomic interaction energy (ANOLEA) score. These parameters help identify important functional regions on the surface of a protein. The last parameter involves the use of a new method for pseudobinding free-energy estimation to specifically probe the importance of residue side-chains to the stability of protein fold. A decision tree was designed to optimally combine these three parameters. The result was compared to the functional data stored in the International Agency for Research on Cancer (IARC) TP53 mutation database. The final prediction achieved a prediction accuracy of 70% and a Matthews correlation coefficient of 0.45. It also showed a high specificity of 91.8%. Mutations in the 85 correctly identified important residues represented 81.7% of the total mutations recorded in the database. In addition, the method was able to correctly assign a probable functional or structural role to the residues. Such information could be critical for the interpretation and prediction of the effect of missense mutations, as it not only provided the fundamental explanation of the observed effect, but also helped design the most appropriate laboratory experiment to verify the prediction results.

Structural motifs of biomolecules.

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularity-free self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.

Structural Analysis of Aggregate Blends Using the SHRP Gyratory Compactor, MLR-95-8, 1996

The Iowa Department of Transportation (IDOT) received a Strategic Highway Research Program (SHRP) gyratory compactor in December 1994. Since then IDOT has been studying the ability of the compactor to analyze fundamental properties of aggregates such as shape, texture, and gradation by studying the volumetrics of the aggregate blends under a standard load using the SHRP gyratory compactor. This method of analyzing the volumetrics of aggregate blends is similar to SHRP's fine aggregate angularity procedure, which analyzes void levels in noncompacted aggregate blends, which in turn can be used to evaluate the texture or shape of aggregates, what SHRP refers to as angularity. Research is showing that by splitting the aggregate blend on the 2.36-mm (#8) sieve and analyzing the volumetrics or angularity of the separated blend, important fundamental properties can be determined. Most important is structure (the degree and location of aggregate interlock). In addition, analysis of the volumes of the coarse and fine portions can predict the voids in the mineral aggregate and the desired asphalt content. By predicting these properties, it can be determined whether the combined aggregate blend, when mixed with asphalt cement, will produce a mix with structural adequacy to carry the designed traffic load.

Maintenance of Pavement Skid Resistance (Open Graded Asphalt Friction Courses), Progress Report, HR-170, 1976

This project involved the evaluation of several aggregates previously rated poor to excellent with respect to skid resistance and certain mix design parameters. An open graded asphalt friction course was evaluated using 4 comparably graded aggregates: quartzite, fine grained limestone, coarse limestone and lightweight expanded shale. The performance investigations involved the verification of observations of the quartzite test sections, evaluation of the effect of blending the superior quartzite with a typical coarse grained-textured limestone, and the evaluation of the limestone. The effects of traffic on the aggregates used in the test sections were studied, as well as the relationship between asphalt content levels and traffic with respect to performance. The bond of the open graded friction course mixture was also evaluated. The SN performance of all test sections after sixteen months of exposure was found to be satisfactory in that none of the material combinations had polished to the point where unacceptable SN levels developed. When material combinations were compared, significant differences were noted.

Dynamic Deflections for Determining Structural Rating of Flexible Pavements, HR-178, 1979

The Road Rater is a dynamic deflection measuring apparatus for flexible base pavements. The Road Rater replaces the Benkelman Beam which was last used by the Iowa DOT in 1977. Road Rater test results correlate reasonably well (correlation coefficient = 0.83) with Benkelman Beam test data. The basic differences between the Road Rater and Benkelman Beam are as follows: 1. The Benkelman Beam uses a static 18,000 lb. load while the Road Rater uses a dynamic 800 to 2,000 lb. loading. 2. The Road Rater tests much faster and more economically than the Benkelman Beam. 3. The Road Rater better simulates a moving truck than the Benkelman Beam. The basic operating principle of the Road Rater is to impart a dynamic loading and measure the resultant movement of the pavement with velocity sensors. This data, when properly adjusted for temperature by use of a nomograph included in this report, can be used to determine pavement life expectancy and estimate overlay thickness required. Road Rater testing will be conducted in the spring, when pavements are in their weakest condition, until seasonal correction factors can be developed. The Road Rater does not have sufficient ram weight to effectively evaluate load carrying capacity of rigid pavements. All rigid pavements react similarly to Road Rater testing and generally deflect from 0.65 to 1.30 mils. Research will be contined to evaluate rigid pavements with the Road Rater, however. The Road Rater has proven to be a reliable, troublefree pavement evaluation machine. The deflection apparatus was originally front-mounted,but was rear-mounted during the winter of 1977-78. Since that time, van handling has greatly improved, and front suspension parts are no longer overstressed due to improper weight distribution.

The effect of mutations in the DRY motif on the constitutive activity and structural instability of the histamine H(2) receptor.

In previous studies we showed that the wild-type histamine H(2) receptor stably expressed in Chinese hamster ovary cells is constitutively active. Because constitutive activity of the H(2) receptor is already found at low expression levels (300 fmol/mg protein) this receptor is a relatively unique member of the G-protein-coupled receptor (GPCR) family and a useful tool for studying GPCR activation. In this study the role of the highly conserved DRY motif in activation of the H(2) receptor was investigated. Mutation of the aspartate 115 residue in this motif resulted in H(2) receptors with high constitutive activity, increased agonist affinity, and increased signaling properties. In addition, the mutant receptors were shown to be highly structurally instable. Mutation of the arginine 116 residue in the DRY motif resulted also in a highly structurally instable receptor; expression of the receptor could only be detected after stabilization with either an agonist or inverse agonist. Moreover, the agonist affinity at the Arg-116 mutant receptors was increased, whereas the signal transduction properties of these receptors were decreased. We conclude that the Arg-116 mutant receptors can adopt an active conformation but have a decreased ability to couple to or activate the G(s)-protein. This study examines the pivotal role of the aspartate and arginine residues of the DRY motif in GPCR function. Disruption of receptor stabilizing constraints by mutation in the DRY motif leads to the formation of active GPCR conformations, but concomitantly to GPCR instability.

Maintenance of A/P body regions in planarians by TCEN49, a putative cystine-knot neurotrophin.

In freshwater planarians, the protein TCEN49 has been linked to the regional specification of the central body region, which includes the pharynx.

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Studies of the structural basis of protein thermostability have produced a confusing picture. Small sets of proteins have been analyzed from a variety of thermophilic species, suggesting different structural features as responsible for protein thermostability. Taking advantage of the recent advances in structural genomics, we have compiled a relatively large protein structure dataset, which was constructed very carefully and selectively; that is, the dataset contains only experimentally determined structures of proteins from one specific organism, the hyperthermophilic bacterium Thermotoga maritima, and those of close homologs from mesophilic bacteria. In contrast to the conclusions of previous studies, our analyses show that oligomerization order, hydrogen bonds, and secondary structure play minor roles in adaptation to hyperthermophily in bacteria. On the other hand, the data exhibit very significant increases in the density of salt-bridges and in compactness for proteins from T.maritima. The latter effect can be measured by contact order or solvent accessibility, and network analysis shows a specific increase in highly connected residues in this thermophile. These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation.

Spontaneous 24-h GHRELIN secretion pattern in fasting subjects : maintenance of a meal-related pattern

RESUME OBJECTIF: Outre la stimulation de la sécrétion d'hormone de croissance, la ghréline cause une prise pondérale par augmentation de l'assimilation d'aliments et réduction de la consommation lipidique. Il a été décrit que les taux de ghréline augmentent durant la phase pré-prandiale et diminuent juste après un repas, ceci suggérant qu'elle puisse jouer un rôle d'initiateur de la prise du repas. Cependant, la sécrétion de ghréline chez des sujets à jeun n'a pas encore été étudiée en détail. DESSIN: Les profils de sécrétion de ghréline pendant 24 heures ont été étudiés chez six sujets volontaires sains (3 femmes, 3 hommes; 25.5 ans; BMI 22.8 kg/m2) et comparés aux profils plasmatiques de l'hormone de croissance, de l'insuline et du glucose. METHODE: Des échantillons sanguins ont été prélevés toutes les 20 minutes pendant 24 heures et les taux de ghréline ont été mesurés par radio-immuno essai, utilisant un anticorps polyclonal de lapin. Le profil circadien de la sécrétion de ghréline (cluster analysis) a été évalué. RESULTATS: Une augmentation puis une diminution spontanée des taux de ghréline ont été observées aux moments où les sujets auraient habituellement mangé. La ghréline a été sécrétée de façon pulsatile avec approximativement 8 pics par 24 heures. Une diminution générale des taux de ghréline a également été observée durant la période d'étude. Aucune corrélation n'a pu être observée entre les taux de ghréline, d'homione de croissance, d'insuline et de glucose. CONCLUSIONS: Cette étude montre que pendant une période de jeûne les taux de ghréline suivent un profil similaire à ceux décrits chez des sujets mangeant 3 fois par jour. Durant le jeûne, l'hormone de croissance, l'insuline et le glucose ne semblent pas être impliqués dans la régulation de la sécrétion de ghréline. En outre, nous avons observé que la sécrétion de ghréline est pulsatile. La variation des taux de ghréline, indépendamment des repas, chez des sujets à jeun, renforce les observations préalables selon lesquelles le système nerveux central est primairement impliqué dans la régulation de la prise alimentaire. ABSTRACT: OBJECTIVE: Ghrelin stimulates GH release and causes weight gain through increased food intake and reduced fat utiIization. Ghrelin levels were shown to rise in the preprandial period and decrease shortly after meal consumption, suggesting a role as a possible meal initiator. However, ghrelin secretion in fasting subjects has not yet been studied in detail. DESIGN: 24-h ghrelin profiles were studied in six healthy volunteers (three females; 25.5 years; body mass index 22.8 kg/m2) and compared with GH, insulin and glucose levels. METHODS: Blood samples were taken every 20 min during a 24-h fasting period and total ghrelin levels were measured by RIA using a polyclonal rabbit antibody. The circadian pattern of ghrelin secretion and pulsatility (Cluster analysis) were evaluated. RESULTS: An increase and spontaneous decrease in ghrelin were seen at the timepoints of customary meals. Ghrelin was secreted in a pulsatile manner with approximately 8 peaks/24 h. An overall decrease in ghrelin levels was observed during the study period. There was no correlation of ghrelin with GH, insulin or blood glucose levels. CONCLUSIONS: This pilot study indicates that fasting ghrelin profiles display a circadian pattern similar to that described in people eating three times per day. In a fasting condition. GH, insulin and glucose do not appear to be involved in ghrelin regulation. In addition, we round that ghrelin is secreted in a pulsatile pattern. The variation in ghrelin independently of meals in fasting subjects supports previous observations that it is the brain that is primarily involved in the regulation of meal initiation.