Primary culture and mRNA analysis of human ovarian cells

Established cell lines are invaluable for studying cell and molecular biological questions. A variety of human ovarian cancer (OC) cell lines exist, however, most have acquired significant genetic alterations from their cells of origin, including deletion of important cell cycle regulatory genes. In order to analyze signaling events related to cell cycle control in human OC, we have modified existing protocols for isolating and culturing OC cells from patient ascites fluid and normal ovarian surface epithelial (OSE) cells from benign ovarian tissue sections. These cells maintain an epithelial phenotype and can be manipulated experimentally for several passages before cellular senescence. An example using TGFb1 treatment of OC cells to examine signaling and target gene activation is presented

Fixed parameter tractable algorithms in combinatorial topology

To enumerate 3-manifold triangulations with a given property, one typically begins with a set of potential face pairing graphs (also known as dual 1-skeletons), and then attempts to flesh each graph out into full triangulations using an exponential-time enumeration. However, asymptotically most graphs do not result in any 3-manifold triangulation, which leads to significant "wasted time" in topological enumeration algorithms. Here we give a new algorithm to determine whether a given face pairing graph supports any 3-manifold triangulation, and show this to be fixed parameter tractable in the treewidth of the graph. We extend this result to a "meta-theorem" by defining a broad class of properties of triangulations, each with a corresponding fixed parameter tractable existence algorithm. We explicitly implement this algorithm in the most generic setting, and we identify heuristics that in practice are seen to mitigate the large constants that so often occur in parameterised complexity, highlighting the practicality of our techniques.Comment: 16 pages, 9 figure

Finite covers of random 3-manifolds

A 3-manifold is Haken if it contains a topologically essential surface. The Virtual Haken Conjecture posits that every irreducible 3-manifold with infinite fundamental group has a finite cover which is Haken. In this paper, we study random 3-manifolds and their finite covers in an attempt to shed light on this difficult question. In particular, we consider random Heegaard splittings by gluing two handlebodies by the result of a random walk in the mapping class group of a surface. For this model of random 3-manifold, we are able to compute the probabilities that the resulting manifolds have finite covers of particular kinds. Our results contrast with the analogous probabilities for groups coming from random balanced presentations, giving quantitative theorems to the effect that 3-manifold groups have many more finite quotients than random groups. The next natural question is whether these covers have positive betti number. For abelian covers of a fixed type over 3-manifolds of Heegaard genus 2, we show that the probability of positive betti number is 0. In fact, many of these questions boil down to questions about the mapping class group. We are lead to consider the action of mapping class group of a surface S on the set of quotients pi_1(S) -> Q. If Q is a simple group, we show that if the genus of S is large, then this action is very mixing. In particular, the action factors through the alternating group of each orbit. This is analogous to Goldman's theorem that the action of the mapping class group on the SU(2) character variety is ergodic.Comment: 60 pages; v2: minor changes. v3: minor changes; final versio

Draft genome sequences of gammaproteobacterial methanotrophs isolated from marine ecosystems

The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems

Large random simplicial complexes, I

In this paper we introduce a new model of random simplicial complexes depending on multiple probability parameters. This model includes the well-known Linial - Meshulam random simplicial complexes and random clique complexes as special cases. Topological and geometric properties of a multi-parameter random simplicial complex depend on the whole combination of the probability parameters and the thresholds for topological properties are convex sets rather than numbers (as in all previously known models). We discuss the containment properties, density domains and dimension of the random simplicial complexes.Comment: 21 pages, 6 figure

Weak Liouville-Arnold Theorems & Their Implications

This paper studies the existence of invariant smooth Lagrangian graphs for Tonelli Hamiltonian systems with symmetries. In particular, we consider Tonelli Hamiltonians with n independent but not necessarily involutive constants of motion and obtain two theorems reminiscent of the Liouville-Arnold theorem. Moreover, we also obtain results on the structure of the configuration spaces of such systems that are reminiscent of results on the configuration space of completely integrable Tonelli Hamiltonians.Comment: 24 pages, 1 figure; v2 corrects typo in online abstract; v3 includes new title (was: A Weak Liouville-Arnold Theorem), re-arrangement of introduction, re-numbering of main theorems; v4 updates the authors' email and physical addresses, clarifies notation in section 4. Final versio

Facultative methanotrophy: false leads, true results, and suggestions for future research

Methanotrophs are a group of phylogenetically diverse microorganisms characterized by their ability to utilize methane as their sole source of carbon and energy. Early studies suggested that growth on methane could be stimulated with the addition of some small organic acids, but initial efforts to find facultative methanotrophs, i.e., methanotrophs able to utilize compounds with carbon–carbon bonds as sole growth substrates were inconclusive. Recently, however, facultative methanotrophs in the genera Methylocella , Methylocapsa , and Methylocystis have been reported that can grow on acetate, as well as on larger organic acids or ethanol for some species. All identified facultative methanotrophs group within the Alphaproteobacteria and utilize the serine cycle for carbon assimilation from formaldehyde. It is possible that facultative methanotrophs are able to convert acetate into intermediates of the serine cycle (e.g. malate and glyoxylate), because a variety of acetate assimilation pathways convert acetate into these compounds (e.g. the glyoxylate shunt of the tricarboxylic acid cycle, the ethylmalonyl‐CoA pathway, the citramalate cycle, and the methylaspartate cycle). In this review, we summarize the history of facultative methanotrophy, describe scenarios for the basis of facultative methanotrophy, and pose several topics for future research in this area.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86841/1/fml2315.pd

On 3d extensions of AGT relation

An extension of the AGT relation from two to three dimensions begins from connecting the theory on domain wall between some two S-dual SYM models with the 3d Chern-Simons theory. The simplest kind of such a relation would presumably connect traces of the modular kernels in 2d conformal theory with knot invariants. Indeed, the both quantities are very similar, especially if represented as integrals of the products of quantum dilogarithm functions. However, there are also various differences, especially in the "conservation laws" for integration variables, which hold for the monodromy traces, but not for the knot invariants. We also discuss another possibility: interpretation of knot invariants as solutions to the Baxter equations for the relativistic Toda system. This implies another AGT like relation: between 3d Chern-Simons theory and the Nekrasov-Shatashvili limit of the 5d SYM.Comment: 23 page

Management Effects on Greenhouse Gas Dynamics in Fen Ditches

Globally, large areas of peatland have been drained through the digging of ditches, generally to increase agricultural production. By lowering the water table it is often assumed that drainage reduces landscape-scale emissions of methane (CH4) into the atmosphere to negligible levels. However, drainage ditches themselves are known to be sources of CH4 and other greenhouse gases (GHGs), but emissions data are scarce, particularly for carbon dioxide (CO2) and nitrous oxide (N2O), and show high spatial and temporal variability. Here, we report dissolved GHGs and diffusive fluxes of CH4 and CO2 from ditches at three UK lowland fens under different management; semi-natural fen, cropland, and cropland restored to low-intensity grassland. Ditches at all three fens emitted GHGs to the atmosphere, but both fluxes and dissolved GHGs showed extensive variation both seasonally and within-site. CH4 fluxes were particularly large, with medians peaking at all three sites in August at 120-230 mg m-2 d-1. Significant between site differences were detected between the cropland and the other two sites for CO2 flux and all three dissolved GHGs, suggested that intensive agriculture has major effects on ditch biogeochemistry. Multiple regression models using environmental and water chemistry data were able to explain 29-59% of observed variation in dissolved GHGs. Annual CH4 fluxes from the ditches were 37.8, 18.3 and 27.2 g CH4 m-2 yr-1 for the semi-natural, grassland and cropland, and annual CO2 fluxes were similar (1100 to 1440 g CO2 m-2 yr-1) among sites. We suggest that fen ditches are important contributors to landscape-scale GHG emissions, particularly for CH4. Ditch emissions should be included in GHG budgets of human modified fens, particularly where drainage has removed the original terrestrial CH4 source, e.g. agricultural peatlands

A critical interpretive synthesis of evidence and values in recommendations to disinvest from population Screening

• the interplay between values and evidence in screening policy • methods of an ongoing systematic review • examples of disinvestment decision