Variational localized-site cluster expansions. X. Dimerization in linear Heisenberg chains

Ground-state instability to bond alternation in long linear chains is considered from the point of view of valence-bond (VB) theory. This instability is viewed as the consequence of a long-range order (LRO) which is expected if the ground state is reasonably described in terms of the Kekulé states (with nearest-neighbor singlet pairing). It is argued that the bond alternation and associated LRO predicted by this simple, VB picture is retained for certain linear Heisenberg models; many-body VB calculations on spin s=1 / 2 and s=1 chains are carried out in a test of this argument.

Independent contribution of parental migrant status and educational level to adiposity and eating habits in preschool children.

Background/Objective:Little is known about the precise role of parental migrant status (MS) and educational level (EL) on adiposity and various eating habits in young children. Therefore, we assessed their independent contribution in preschoolers.Subjects/Methods:Of 655 randomly selected preschoolers, 542 (5.1±0.6 years; 71% of parental MS and 37% of low parental EL) were analysed. Body composition was measured by bioelectrical impedance. Eating habits were assessed using a semiqualitative food frequency questionnaire and analysed according to five messages developed by the Swiss Society for Nutrition, based on factors implicated in childhood obesity: (1) 'Drinking water and decreasing sweetened drinks', (2) 'Eating fruit and vegetables', (3) 'Decreasing breakfast skipping', (4) 'Reducing fatty and sweet foods' and (5) 'Reducing the intake of meals and snacks in front of television'.Results:Children of migrant and low EL parents had higher body fat, ate more meals and snacks while watching television and had more fruit and fatty foods compared with their respective counterparts (all P0.04). Children of low EL parents also consumed less water and vegetables compared with their counterparts (all P0.04). In most instances, we found an independent contribution of parental MS and EL to adiposity and eating habits. A more pronounced effect was found if both parents were migrants or of low EL. Differences in adiposity and eating habits were relatively similar to the joint parental data when assessed individually for maternal and paternal MS and EL.Conclusions:Parental MS and EL are independently related to adiposity and various eating habits in preschoolers.European Journal of Clinical Nutrition advance online publication, 3 November 2010; doi:10.1038/ejcn.2010.248.

Linkage disequilibrium between a melanin-based colour polymorphism and tail length in the barn owl

A linkage disequilibrium between sexually selected and life history traits can be explained by three mutually non-exclusive mechanisms. Genes coding for two traits may be located close on the same chromosome, genes responsible for variation in one of the trait may pleiotropically alter the other, and non-random pairing with respect to two traits may generate a non-physical linkage disequilibrium between their genes. Knowledge of which of these three mechanisms is responsible for a covariation between two traits is of interest to understand why differently ornamented individuals differ in several phenotypic aspects. In Switzerland, barn owls Tyto alba mate randomly with respect to a colour polymorphism generating a large range of variants between reddish-brown and white, males being lighter coloured than females. Several studies have shown that plumage coloration is not neutral with respect to some life history components. To test whether coloration is genetically associated with body size, partial cross-fostering experiments were performed by exchanging some hatchlings between nests. These experiments showed that darker biological fathers produce longer-tailed offspring. This sex-specific pattern is consistent with the hypothesis of non-physical linkage disequilibrium. In line with this hypothesis, darker coloured males were mated with longer-tailed females, whereas female coloration was not associated with tail length of their mate. The finding that dark nestlings had a longer tail than their pale siblings also supports the physical linkage and pleiotropy hypotheses. Therefore, non-random pairing can generate or strengthen a genetic covariation between a secondary sexual character and a morphological trait.

The role of the vacuolar H+ - ATPase in membrane fusion

RésuméLa H+-ATPase vacuolaire (V-ATPase) est un complexe enzymatique composé de deux secteurs multimériques (VQ et Vi) dont l'association dans la cellule est réversible. Le secteur intramembranaire de la V-ATPase (V0) interagit physiquement avec des protéines SNARE et stimule la fusion homotypique des vacuoles de la levure (lysosomes), la sécrétion de neurotransmetteurs et d'insuline, la fusion entre phagosome et lysosome ainsi que la sécrétion des corps multivésiculaires par un mécanisme inconnu. Dans cette étude j'ai identifié des résidues d'acides amines situés dans des sous-unités de V0 impliqués dans le mécanisme de fusion des vacuoles mais non essentiels pour l'acidification vacuolaire par la V-ATPase. j'ai utilisé un protocole de mutagenèse aléatoire pour produire des libraries de mutants des sous unités de V0. Ces libraries ont été analysées in vivo afin d'identifier des alleles qui permettent la translocation des protons mais produisent une vacuole fragmentée, phénotype indiquant un défaut dans la fusion membranaire. Les vacuoles des mutants ont été isolées et caractéisées en utilisant une grande variété d'outils biochimiques pour déterminer précisément l'impact des différentes mutations sur l'accomplissement d'événements clés du processus de fusion.J'ai identifié des mutations associées à des défauts spécifiques de la fusion dans plusieurs sous-unités de V0. Dans les protéolipides c, c' et c" ces mutations se concentrent dans la partie cytosolique des domaines transmembranaires. Elles renforcent les associations entre les secteurs de la V-ATPase et entre V0 et les SNAREs. Dans la fusion vacuolaire ces mutations permettent la formation de complexes SNAREs en trans mais inhibent l'induction de la fusion. Par contre, la deletion de la sous- unité d influence les étapes de la fusion qui précèdent la formation des complexes trans-SNAREs. Mes résultats démontrent que V0 joue des rôles différents dans plusieurs étapes de la fusion et que ces fonctions sont liées au système des SNAREs. Ils différencient génétiquement les activités de V0 dans la translocation des protons et dans la fusion et identifient de nombreux résidus importants pour la fusion vacuolaire. De plus, compte tenu de la grande conservation de sequence des protéolipides chez les eukaryotes les mutations identifiées dans cette l'étude apportent de nouvelles informations pour analyser la fonction de V0 dans des organismes multicellulaires pour lesquels la function catalytique de la V-ATPase est essentielle à la survie.Résumé pour le large publicLe transport de protéines et de membranes est important pour maintenir la fonction des organelles dans la cellule. Il s'excerce au niveau des vesicules. La fusion membranaire est un processus élémentaire de ce transport. Pour fusionner deux membranes, il faut la coordination de deux activités: le rapprochement et la déstabiiization des deux membranes. La collaboration d'un ensemble de proteins conservés chez les eukaryotes, est nécessaire pour catalyser ces activités. Les proteins SNAREs sont les protagonistes principaux dans la fusion membranaire. Néanmoins, d'autres protéines, comme des Rab-GTPases et des chaperonnes, sont nécessaires pour permettre ce phénomène de fusion. Toutes ces protéines sont temporairement associées avec les SNAREs et leur fonction dans la fusion membranaire est souvent directement liée à leur activité dans cette association. Le secteur transmembranaire V0 de la V-ATPase rnteragit avec des SNAREs et est essentiel pour la fusion dans une variété de systèmes modèles comme la mouche, la souris et la levure. Le secteur V0 est composé de six protéines différentes. Avec te secteur Va, qui réside dans le cytosol, il forme la V-ATPase dont la fonction principale est l'acidification des organelles par translocation des protons à travers la membrane par un mécanisme ressemblant à celui d'une pompe. V0joue un role dans la fusion membranaire, indépendamment de son activité catalytique liée au pompage des protons, et ce rôle est encore largement méconnu à ce jour. Le but de ma thèse était de mieux comprendre l'implication de V0 dans ce contexte.Pour étudier des activités liées à la V-ATPase, la levure est un excellent modèle d'étude car elle survie à une inactivation de l'enzyme alors que le meme traitement serait léthal pour des organismes multicellulaires. Dans ma thèse j'ai utilisé la fusion homotypique de la vacuole de levure comme système modèle pour étudier le rôle de V0 dans la fusion. J'ai muté des gènes qui encodent des sous- unités de V0 et les ai introduit dans des souches privées des gènes respectifs. Dans les librairies de souches portant différentes versions de ces gènes j'ai cherché des clones exprimant une V-ATPase intacte et fonctionnelle mais qui possèdent une vacuole fragmentée. Le plus souvent, une vacuole fragmentée indique un défaut dans la fusion vacuolaire. Dans les trois types de protéolipides qui composent un cylindre dans le secteur V0, j'ai trouvé des clones avec une vacuole fragmentée. Après avoir isolé les mutations responsable de ce type de morphologie vacuolaire, j'ai isolé les vacuoles de ces clones pour étudier leur activités dans différentes étapes de la fusion vacuolaire. Les résultats de ces analyses mettent en évidence une implication de V0 dans plusieurs étapes de la fusion vacuolaire. Certaines mutations sélectionnées dans mon étude inhibent une étape précoce de la fusion qui inclue la dissociation des complexes SNARE, tandis que d'autres mutations inhibent une étape tardive du processus de fusion qui inclue la transmission d'une force disruptive dans la membrane.AbstractThe membrane-integral V0 sector of the vacuolar H+-ATPase (V-ATPase) interacts with SNARE proteins. V0 stimulates fusion between yeast vacuoles (lysosomes) (Peters et al., 2001b), secretion of neurotransmitters and insulin (Hiesinger et al., 2005a, Sun-Wada et al., 2006a), phagosome-lysosome fusion (Peri and Nusslein-Volhard, 2008) and secretion of multivesicular bodies (Liegeois et al., 2006b) by a yet unknown mechanism. In my thesis, I identified sites in V0 subunits that are involved in yeast vacuole fusion but dispensable for the proton pumping by the V-ATPase. I randomly mutagenized V0 subunits and screened in vivo for mutant alleles that support proton pumping but cause fragmented vacuoles, a phenotype indicative of a fusion defect. Mutant vacuoles were isolated and analyzed in a cell-free system, allowing assay of key events in fusion, such as trans-SNARE pairing, lipid transition and fusion pore opening (Reese et al., 2005b).Mutants with selective fusion defects were found in several V0 subunits. In the proteolipids c, c' and c", critical mutations are concentated in the cytosolic half of the transmembrane domains. These mutations rendered the V-ATPase holoenzyme more stable and modulated V0-SNARE associations. In vacuole fusion critical proteolipid mutations permitted trans-SNARE pairing but impeded the induction of lipid flow between the membranes. Deletion of subunit d, by contrast, influenced early stages of fusion that precede trans-SNARE pairing. My results show that V0 acts in several steps of the fusion process and that its function is intimately connected to the SNARE system. They genetically separate the proton pump and fusion activities of V0 and identify numerous critical residues. Given the high sequence conservation of proteolipids in eukaryotic life, the identified mutations may be helpful in analyzing the fusion function of V0 also in mammalian cells, where V- ATPase pump function is essential for survival.

MHC-genotype of progeny influenced by parental infection.

In a previous series of in vitro fertilization experiments with mice we found non-random combination of major histocompatibility complex (MHC) haplotypes in the very early embryos. Our results suggested that two selection mechanisms were operating: (i) the eggs selected specific sperm; and (ii) the second meiotic division in the eggs was influenced by the type of sperm that entered the egg. Furthermore, the proportion of MHC-heterozygous embryos varied over time, suggesting that non-random fertilization was dependent on an external factor that changed over time. As a higher frequency of heterozygous individuals correlated with an uncontrolled epidemic by MHV (mouse hepatitis virus), we suggested that MHV-infection might have influenced the outcome of fertilization. Here, we present an experiment that tests this hypothesis. We infected randomly chosen mice with MHV and sham-infected control mice five days before pairing. We recovered the two-cell embryos from the oviduct, cultured them until the blastocyst stage, and determined the genotype of each resulting blastocyst by polymerase chain reaction. We found the pattern that we expected from our previous experiments: virus-infected mice produced more MHC-heterozygous embryos than sham-infected ones. This suggests that parents are able to promote specific combinations of MHC-haplotypes during fertilization according to the presence or absence of a viral infection.

Three-stranded DNA structure; is this the secret of DNA homologous recognition?

A novel type of triple-stranded DNA structure was proposed by several groups to play a crucial role in homologous recognition between single- and double-stranded DNA molecules. In this still putative structure a duplex DNA was proposed to co-ordinate a homologous single strand in its major groove side. In contrast to the well-characterized pyrimidine-purine-pyrimidine triplexes in which the two like strands are antiparallel and which are restricted to poly-pyrimidine-containing stretches, the homology-specific triplexes would have like strands in parallel orientation and would not be restricted to any particular sequence provided that there is a homology between interacting DNA molecules. For many years the stereo-chemical possibility of forming homology-dependent three- or four-stranded DNA structures during the pairing stage of recombination reactions was seriously considered in published papers. However, only recently has there been a marked increase in the number of papers that have directly tested the formation of triple-stranded DNA structures during the actual pairing stage of the recombination reaction. Unfortunately the results of these tests are not totally clear cut; while some laboratories presented experimental evidence consistent with the formation of triplexes, others studying the same or very similar systems offered alternative explanations. The aim of this review is to present the current state of the central question in the mechanism of homologous recombination, namely, what kind of DNA structure is responsible for DNA homologous recognition. Is it a novel triplex structure or just a classical duplex?

Coexpression of the T-cell receptor constant alpha domain triggers tumor reactivity of single-chain TCR-transduced human T cells.

Transfer of tumor antigen-specific T-cell receptors (TCRs) into human T cells aims at redirecting their cytotoxicity toward tumors. Efficacy and safety may be affected by pairing of natural and introduced TCRalpha/beta chains potentially leading to autoimmunity. We hypothesized that a novel single-chain (sc)TCR framework relying on the coexpression of the TCRalpha constant alpha (Calpha) domain would prevent undesired pairing while preserving structural and functional similarity to a fully assembled double-chain (dc)TCR/CD3 complex. We confirmed this hypothesis for a murine p53-specific scTCR. Substantial effector function was observed only in the presence of a murine Calpha domain preceded by a TCRalpha signal peptide for shuttling to the cell membrane. The generalization to a human gp100-specific TCR required the murinization of both C domains. Structural and functional T-cell avidities of an accessory disulfide-linked scTCR gp100/Calpha were higher than those of a dcTCR. Antigen-dependent phosphorylation of the proximal effector zeta-chain-associated protein kinase 70 at tyrosine 319 was not impaired, reflecting its molecular integrity in signaling. In melanoma-engrafted nonobese diabetic/severe combined immunodeficient mice, adoptive transfer of scTCR gp100/Calpha transduced T cells conferred superior delay in tumor growth among primary and long-term secondary tumor challenges. We conclude that the novel scTCR constitutes a reliable means to immunotherapeutically target hematologic malignancies.

KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading.

Krüppel-associated box domain-zinc finger proteins (KRAB-ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB-mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB-containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB-mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 beta (HP1beta) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1-dependent transcriptional repression at an endogenous KRAB-ZFP gene cluster, where KAP1 binds to the 3' end of genes and mediates propagation of H3K9me3 and HP1beta towards their 5' end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB-ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB-ZFPs and KAP1.

Predicting the mating system from phenotypic correlations between life-history and sperm quality traits in the Alpine whitefish Coregonus zugensis

The mating behavior and reproductive strategies of Alpine whitefish like Coregonus zugensis (Nusslin) are poorly understood, probably because they spawn in deep water where direct observations are difficult. In this study, we interpret life-history and sperm quality traits of fish that we caught from their spawning place. We found that males invest heavily into gonadal tissue (up to 5.6% of their body weight), which is, in comparison to other fish, consistent with external fertilization, distinct pairing and moderate to high communal spawning, or no pairing and low to moderate communal spawning. Sperm competition theory and recent experimental studies on other salmonids predict that males optimize ejaculate characteristics in relation to the costs of sperm and the level of competition they have to expect: dominant males are predicted to invest less into ejaculate quality and to have slower spermatozoa than subdominant males. We found that spermatozoa of older males are slower than those of younger males. Moreover, older males have larger breeding tubercles, a secondary sexual trait that has, in some previous studies, been found to be linked to good condition and to good genetic quality. Our results suggest that C. zugensis has age-linked reproductive strategies, that multimale spawning is common, i.e., that sperm competition plays a significant role, and that older males are on average dominant over younger males at the spawning place.

Saccharomyces cerevisiae Dmc1 and Rad51 Proteins Preferentially Function with Tid1 and Rad54 Proteins, Respectively, to Promote DNA Strand Invasion during Genetic Recombination.

The Saccharomyces cerevisiae Dmc1 and Tid1 proteins are required for the pairing of homologous chromosomes during meiotic recombination. This pairing is the precursor to the formation of crossovers between homologs, an event that is necessary for the accurate segregation of chromosomes. Failure to form crossovers can have serious consequences and may lead to chromosomal imbalance. Dmc1, a meiosis-specific paralog of Rad51, mediates the pairing of homologous chromosomes. Tid1, a Rad54 paralog, although not meiosis-specific, interacts with Dmc1 and promotes crossover formation between homologs. In this study, we show that purified Dmc1 and Tid1 interact physically and functionally. Dmc1 forms stable nucleoprotein filaments that can mediate DNA strand invasion. Tid1 stimulates Dmc1-mediated formation of joint molecules. Under conditions optimal for Dmc1 reactions, Rad51 is specifically stimulated by Rad54, establishing that Dmc1-Tid1 and Rad51-Rad54 function as specific pairs. Physical interaction studies show that specificity in function is not dictated by direct interactions between the proteins. Our data are consistent with the hypothesis that Rad51-Rad54 function together to promote intersister DNA strand exchange, whereas Dmc1-Tid1 tilt the bias toward interhomolog DNA strand exchange.

Consommation d'aliments riches en calcium dans la population adulte de Suisse romande et du Tessin. [Consumption of calcium-rich food in the adult population of French-speaking Switzerland and of Tessin].

Food intake high in calcium content is important in the development of skeleton and the prevention of osteoporosis. From a public health perspective, it is therefore important to know the dietary calcium intake of a population. Two population surveys in the French and Italian parts of Switzerland (MONICA, 1988-1989, and Geneva, 1991), were combined to study nutritional habits related to calcium intake. A random population sample, aged 35 et 65 years, answered to a 24 hour recall questionnaire, either self-administered (MONICA, cantons of Vaud, Fribourg and Tessin, N = 2734) or by phone (canton of Geneva, N = 475). In the 4 cantons, for the previous day, 60% of participants ate dairy products, particularly whole milk and cheese. They drunk 3-4 dl/day of milk. A significant proportion (10%) of french and italian speaking Swiss did not consume any food high in calcium content. In Geneva, the mean daily calcium intake was 656 mg in men and 489 mg in women. In conclusion 1) eating habits related to calcium intake are similar across cantons; 2) women consume dairy products more frequently than men, but in smaller quantities; 3) about 60% of men and 80% of women do not get the daily amount of calcium recommended for the prevention of osteoporosis.

Differences in aerobic fitness and lifestyle characteristics in preschoolers according to their weight status and sports club participation.

Objective: This study assesses differences in adiposity, aerobic fitness, and lifestyle characteristics in preschoolers according to their weight status and sports club (SC) participation. Method: As part of the Ballabeina study, 600 randomly selected preschoolers (mean age 5.1 ± 0.6 years; 50.2% girls) were analyzed. Body composition was measured by bioelectrical impedance, aerobic fitness by the 20-meter shuttle run test, and physical activity by accelerometers. Eating habits, media use, and SC participation were assessed by questionnaires. Results: Overweight children (Swiss national percentiles) and children not participating in SC had both lower aerobic fitness and higher % body fat compared to their respective counterparts (all p ≤ 0.028). In addition, children not participating in SC were less physically active, had more media use, and ate less healthy compared to children participating in SC (all p ≤ 0.023). Controlling for parental sociocultural determinants attenuated differences in % body fat, in physical activity, and in eating habits. Conclusion: Aerobic fitness differs both according to weight status and SC participation in preschoolers. Furthermore, in view of the many differences in lifestyle behaviors, SC participation at this age could represent a more discriminatory indicator of healthy lifestyle characteristics than weight status.

The V-ATPase proteolipid cylinder promotes the lipid-mixing stage of SNARE-dependent fusion of yeast vacuoles.

The V-ATPase V(0) sector associates with the peripheral V(1) sector to form a proton pump. V(0) alone has an additional function, facilitating membrane fusion in the endocytic and late exocytic pathways. V(0) contains a hexameric proteolipid cylinder, which might support fusion as proposed in proteinaceous pore models. To test this, we randomly mutagenized proteolipids. We recovered alleles that preserve proton translocation, normal SNARE activation and trans-SNARE pairing but that impair lipid and content mixing. Critical residues were found in all subunits of the proteolipid ring. They concentrate within the bilayer, close to the ring subunit interfaces. The fusion-impairing proteolipid substitutions stabilize the interaction of V(0) with V(1). Deletion of the vacuolar v-SNARE Nyv1 has the same effect, suggesting that both types of mutations similarly alter the conformation of V(0). Also covalent linkage of subunits in the proteolipid cylinder blocks vacuole fusion. We propose that a SNARE-dependent conformational change in V(0) proteolipids might stimulate fusion by creating a hydrophobic crevice that promotes lipid reorientation and formation of a lipidic fusion pore.

Study of chromosome rearrangements associated with the trpE26 mutation of Bacillus subtilis.

Chromosome rearrangements involved in the formation of merodiploid strains in the Bacillus subtilis 168-166 system were explained by postulating the existence of intrachromosomal homology regions. This working hypothesis was tested by analysing sequences and restriction patterns of the, as yet uncharacterized, junctions between chromosome segments undergoing rearrangements in parent, 168 trpC2 and 166 trpE26, as well as in derived merodiploid strains. Identification, at the Ia/Ib chromosome junction of both parent strains, of a 1.3 kb segment nearly identical to a segment of prophage SPbeta established the existence of one of the postulated homology sequences. Inspection of relevant junctions revealed that a set of different homology regions, derived from prophage SPbeta, plays a key role in the formation of so-called trpE30, trpE30+, as well as of new class I merodiploids. Analysis of junctions involved in the transfer of the trpE26 mutation, i.e. simultaneous translocation of chromosome segment C and rotation of the terminal relative to the origin moiety of the chromosome, did not confirm the presence of any sequence suitable for homologous recombination. We propose a model involving simultaneous introduction of four donor DNA molecules, each comprising a different relevant junction, and their pairing with the junction regions of the recipient chromosome. The resolution of this structure, resting on homologous recombination, would confer the donor chromosome structure to the recipient, achieving some kind of 'transstamping'. In addition, a rather regular pattern of inverse and direct short sequence repeats in regions flanking the breaking points could be correlated with the initial, X-ray-induced, rearrangement.

Similarity in food cleaning techniques within matrilines in wild vervet monkeys.

Social learning and the formation of traditions rely on the ability and willingness to copy one another. A central question is under which conditions individuals adapt behaviour to social influences. Here, we demonstrate that similarities in food processing techniques emerge on the level of matrilines (mother-offspring) but not on the group level in an experiment on six groups of wild vervet monkeys that involved grapes covered with sand. Monkeys regularly ate unclean grapes but also used four cleaning techniques more similarly within matrilines: rubbing in hands, rubbing on substrate, open with mouth, and open with hands. Individual cleaning techniques evolved over time as they converged within matrilines, stabilised at the end and remained stable in a follow-up session more than one year later. The similarity within matrilines persisted when we analyzed only foraging events of individuals in the absence of other matriline members and matriline members used more similar methods than adult full sisters. Thus, momentary conversion or purely genetic causation are unlikely explanations, favouring social learning as mechanism for within matriline similarities. The restriction of traditions to matriline membership rather than to the group level may restrict the development of culture in monkeys relative to apes or humans.