Hamiltonian flows for pseudo-Anosov mapping classes

For a given pseudo-Anosov homeomorphism $\phi$ of a closed surface $S$, the action of $\phi$ on the Teichm\"uller space $\mathcal T(S)$ is an automorphism of the complex structure preserving the Weil-Petersson-Goldman symplectic form. We give explicit formulae for two invariant functions $\mathcal T(S)\to \mathbb R$ whose symplectic gradients generate autonomous Hamiltonian flows that coincide with the action of $\phi$ at time one. We compute the Poisson bracket of these two functions, which essentially amounts to computing the variation of length of a H\"older cocyle on one lamination along the shear vector field defined by another. For a measurably generic set of laminations, we prove that the variation of length is expressed as the cosine of the angle between the two laminations integrated against the product H\"older distribution, generalizing a result of Kerckhoff. We also obtain rates of convergence for the supports of germs of differentiable paths of measured laminations in the Hausdorff metric on a hyperbolic surface, which may be of independent interest.Comment: 31 page

Algorithms for detecting dependencies and rigid subsystems for CAD

Geometric constraint systems underly popular Computer Aided Design soft- ware. Automated approaches for detecting dependencies in a design are critical for developing robust solvers and providing informative user feedback, and we provide algorithms for two types of dependencies. First, we give a pebble game algorithm for detecting generic dependencies. Then, we focus on identifying the "special positions" of a design in which generically independent constraints become dependent. We present combinatorial algorithms for identifying subgraphs associated to factors of a particular polynomial, whose vanishing indicates a special position and resulting dependency. Further factoring in the Grassmann- Cayley algebra may allow a geometric interpretation giving conditions (e.g., "these two lines being parallel cause a dependency") determining the special position.Comment: 37 pages, 14 figures (v2 is an expanded version of an AGD'14 abstract based on v1

X Chromosome Evolution in Cetartiodactyla

The mammalian X chromosome is characterized by high level of conservation. On the contrary the Cetartiodactyl X chromosome displays variation in morphology and G-banding pattern. It is hypothesized that X chromosome has undergone multiple rearrangements during Cetartiodactyla speciation. To investigate the evolution of this sex chromosome we have selected 26 BAC clones from cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution maps were obtained by fluorescence in situ hybridisation in a representative range of cetartiodactyl species from different families: pig (Suidae), gray whale (Eschrichtiidae), pilot whale (Delphinidae), hippopotamus (Hippopotamidae), Java mouse deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), giraffe (Giraffidae). To trace the X chromosome evolution during fast radiation in speciose families, we mapped more than one species in Cervidae (moose, Siberian roe deer, fallow deer and Pere David’s deer) and Bovidae (musk ox, goat, sheep, sable antelope, nilgau, gaur, saola, and cattle). We have identified three major conserved synteny blocks and based on this data reconstructed the structure of putative ancestral cetartiodactyl X chromosome. We demonstrate that intrachromosomal rearrangements such as inversions and centromere reposition are main drivers of cetartiodactyl’s chromosome X evolution

X Chromosome Evolution in Cetartiodactyla

The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. To trace the X chromosome evolution during fast radiation in specious families, we performed mapping in several cervids (moose, Siberian roe deer, fallow deer, and Pere David’s deer) and bovid (muskox, goat, sheep, sable antelope, and cattle) species. We have identified three major conserved synteny blocks and rearrangements in different cetartiodactyl lineages and found that the recently described phenomenon of the evolutionary new centromere emergence has taken place in the X chromosome evolution of Cetartiodactyla at least five times. We propose the structure of the putative ancestral cetartiodactyl X chromosome by reconstructing the order of syntenic segments and centromere position for key groups

Gender Differences in Russian Colour Naming

In the present study we explored Russian colour naming in a web-based psycholinguistic experiment (http://www.colournaming.com). Colour singletons representing the Munsell Color Solid (N=600 in total) were presented on a computer monitor and named using an unconstrained colour-naming method. Respondents were Russian speakers (N=713). For gender-split equal-size samples (NF=333, NM=333) we estimated and compared (i) location of centroids of 12 Russian basic colour terms (BCTs); (ii) the number of words in colour descriptors; (iii) occurrences of BCTs most frequent non-BCTs. We found a close correspondence between females’ and males’ BCT centroids. Among individual BCTs, the highest inter-gender agreement was for seryj ‘grey’ and goluboj ‘light blue’, while the lowest was for sinij ‘dark blue’ and krasnyj ‘red’. Females revealed a significantly richer repertory of distinct colour descriptors, with great variety of monolexemic non-BCTs and “fancy” colour names; in comparison, males offered relatively more BCTs or their compounds. Along with these measures, we gauged denotata of most frequent CTs, reflected by linguistic segmentation of colour space, by employing a synthetic observer trained by gender-specific responses. This psycholinguistic representation revealed females’ more refined linguistic segmentation, compared to males, with higher linguistic density predominantly along the redgreen axis of colour space

Subcellular analysis of starch metabolism in developing barley seeds using a non-aqueous fractionation method

Compartmentation of metabolism in developing seeds is poorly understood due to the lack of data on metabolite distributions at the subcellular level. In this report, a non-aqueous fractionation method is described that allows subcellular concentrations of metabolites in developing barley endosperm to be calculated. (i) Analysis of subcellular volumes in developing endosperm using micrographs shows that plastids and cytosol occupy 50.5% and 49.9% of the total cell volume, respectively, while vacuoles and mitochondria can be neglected. (ii) By using non-aqueous fractionation, subcellular distribution between the cytosol and plastid of the levels of metabolites involved in sucrose degradation, starch synthesis, and respiration were determined. With the exception of ADP and AMP which were mainly located in the plastid, most other metabolites of carbon and energy metabolism were mainly located outside the plastid in the cytosolic compartment. (iii) In developing barley endosperm, the ultimate precursor of starch, ADPglucose (ADPGlc), was mainly located in the cytosol (80–90%), which was opposite to the situation in growing potato tubers where ADPGlc was almost exclusively located in the plastid (98%). This reflects the different subcellular distribution of ADPGlc pyrophosphorylase (AGPase) in these tissues. (iv) Cytosolic concentrations of ADPGlc were found to be close to the published Km values of AGPase and the ADPGlc/ADP transporter at the plastid envelope. Also the concentrations of the reaction partners glucose-1-phosphate, ATP, and inorganic pyrophosphate were close to the respective Km values of AGPase. (v) Knock-out of cytosolic AGPase in Riso16 mutants led to a strong decrease in ADPGlc level, in both the cytosol and plastid, whereas knock-down of the ADPGlc/ADP transporter led to a large shift in the intracellular distribution of ADPGlc. (v) The thermodynamic structure of the pathway of sucrose to starch was determined by calculating the mass–action ratios of all the steps in the pathway. The data show that AGPase is close to equilibrium, in both the cytosol and plastid, whereas the ADPGlc/ADP transporter is strongly displaced from equilibrium in vivo. This is in contrast to most other tissues, including leaves and potato tubers. (vi) Results indicate transport rather than synthesis of ADPGlc to be the major regulatory site of starch synthesis in barley endosperm. The reversibility of AGPase in the plastid has important implications for the regulation of carbon partitioning between different biosynthetic pathways

Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae

Peroxisomes undergo rapid, selective autophagic degradation (pexophagy) when the metabolic pathways they contain are no longer required for cellular metabolism. Pex3 is central to the formation of peroxisomes and their segregation because it recruits factors specific for these functions. Here, we describe a novel Saccharomyces cerevisiae protein that interacts with Pex3 at the peroxisomal membrane. We name this protein Atg36 as its absence blocks pexophagy, and its overexpression induces pexophagy. We have isolated pex3 alleles blocked specifically in pexophagy that cannot recruit Atg36 to peroxisomes. Atg36 is recruited to mitochondria if Pex3 is redirected there, where it restores mitophagy in cells lacking the mitophagy receptor Atg32. Furthermore, Atg36 binds Atg8 and the adaptor Atg11 that links receptors for selective types of autophagy to the core autophagy machinery. Atg36 delivers peroxisomes to the preautophagosomal structure before being internalised into the vacuole with peroxisomes. We conclude that Pex3 recruits the pexophagy receptor Atg36. This reinforces the pivotal role played by Pex3 in coordinating the size of the peroxisome pool, and establishes its role in pexophagy in S. cerevisiae