Optimization of DNA extraction from human urinary samples for mycobiome community profiling.

IntroductionRecent data suggest the urinary tract hosts a microbial community of varying composition, even in the absence of infection. Culture-independent methodologies, such as next-generation sequencing of conserved ribosomal DNA sequences, provide an expansive look at these communities, identifying both common commensals and fastidious organisms. A fundamental challenge has been the isolation of DNA representative of the entire resident microbial community, including fungi.Materials and methodsWe evaluated multiple modifications of commonly-used DNA extraction procedures using standardized male and female urine samples, comparing resulting overall, fungal and bacterial DNA yields by quantitative PCR. After identifying protocol modifications that increased DNA yields (lyticase/lysozyme digestion, bead beating, boil/freeze cycles, proteinase K treatment, and carrier DNA use), all modifications were combined for systematic confirmation of optimal protocol conditions. This optimized protocol was tested against commercially available methodologies to compare overall and microbial DNA yields, community representation and diversity by next-generation sequencing (NGS).ResultsOverall and fungal-specific DNA yields from standardized urine samples demonstrated that microbial abundances differed significantly among the eight methods used. Methodologies that included multiple disruption steps, including enzymatic, mechanical, and thermal disruption and proteinase digestion, particularly in combination with small volume processing and pooling steps, provided more comprehensive representation of the range of bacterial and fungal species. Concentration of larger volume urine specimens at low speed centrifugation proved highly effective, increasing resulting DNA levels and providing greater microbial representation and diversity.ConclusionsAlterations in the methodology of urine storage, preparation, and DNA processing improve microbial community profiling using culture-independent sequencing methods. Our optimized protocol for DNA extraction from urine samples provided improved fungal community representation. Use of this technique resulted in equivalent representation of the bacterial populations as well, making this a useful technique for the concurrent evaluation of bacterial and fungal populations by NGS

The Ecoregional Approach to Research in the CGIAR

Report of a joint TAC/Center Directors working group on the implementation of the ecoregional approach by the CGIAR. The document also contains comments by the center directors and by TAC. It was discussed at TAC 60, at a technical consultation organized by SPAAR in April 1993 (report in the collection), and a work shop following the CGIAR meeting of May 1993 (not reported). These discussions were considered at TAC 61. The report describes the evolution of the ecoregional concept during TAC's review of CGIAR priorities and strategies. The approach was seen as a means of conducting applied and strategic research on sustainable production in regions defined by ecological type, drawing on global research for that purpose, and strengthening cooperation with NARS and internationally. Responses from centers are summarized. The paper explores a research model for this purpose, and discusses possible operational models. It also discusses IARC measures to incorporate the ecoregional approach into their medium term plans. The working group doubts that any single operational approach will suit all regions needs. Annexed to the report are a synthesis of TAC's views of the concept, an overview of current and proposed center activities, and the terms of reference of the working group

Mixed axion/neutralino cold dark matter in supersymmetric models

We consider supersymmetric (SUSY) models wherein the strong CP problem is solved by the Peccei-Quinn (PQ) mechanism with a concommitant axion/axino supermultiplet. We examine R-parity conserving models where the neutralino is the lightest SUSY particle, so that a mixture of neutralinos and axions serve as cold dark matter. The mixed axion/neutralino CDM scenario can match the measured dark matter abundance for SUSY models which typically give too low a value of the usual thermal neutralino abundance, such as models with wino-like or higgsino-like dark matter. The usual thermal neutralino abundance can be greatly enhanced by the decay of thermally-produced axinos to neutralinos, followed by neutralino re-annihilation at temperatures much lower than freeze-out. In this case, the relic density is usually neutralino dominated, and goes as \sim (f_a/N)/m_{axino}^{3/2}. If axino decay occurs before neutralino freeze-out, then instead the neutralino abundance can be augmented by relic axions to match the measured abundance. Entropy production from late-time axino decays can diminish the axion abundance, but ultimately not the neutralino abundance. In mixed axion/neutralino CDM models, it may be possible to detect both a WIMP and an axion as dark matter relics. We also discuss possible modifications of our results due to production and decay of saxions. In the appendices, we present expressions for the Hubble expansion rate and the axion and neutralino relic densities in radiation, matter and decaying-particle dominated universes.Comment: 31 pages including 21 figure

Wigner's DD-matrix elements for SU(3)SU(3) - A Generating Function Approach

A generating function for the Wigner's $D$-matrix elements of $SU(3)$ is derived. From this an explicit expression for the individual matrix elements is obtained in a closed form.Comment: RevTex 3.0, 22 pages, no figure

Nanopercolation

We investigate through direct molecular mechanics calculations the geometrical properties of hydrocarbon mantles subjected to percolation disorder. We show that the structures of mantles generated at the critical percolation point have a fractal dimension $d_{f} \approx 2.5$. In addition, the solvent access surface $A_{s}$ and volume $V_{s}$ of these molecules follow power-law behavior, $A_{s} \sim L^{\alpha_A}$ and $V_{s} \sim L^{\alpha_V}$, where $L$ is the system size, and with both critical exponents $\alpha_A$ and $\alpha_V$ being significantly dependent on the radius of the accessing probing molecule, $r_{p}$. Our results from extensive simulations with two distinct microscopic topologies (i.e., square and honeycomb) indicate the consistency of the statistical analysis and confirm the self-similar characteristic of the percolating hydrocarbons. Due to their highly branched topology, some of the potential applications for this new class of disordered molecules include drug delivery, catalysis, and supramolecular structures.Comment: 4 pages, 5 figure

Quantum gravity and the standard model

We show that a class of background independent models of quantum spacetime have local excitations that can be mapped to the first generation fermions of the standard model of particle physics. These states propagate coherently as they can be shown to be noiseless subsystems of the microscopic quantum dynamics. These are identified in terms of certain patterns of braiding of graphs, thus giving a quantum gravitational foundation for the topological preon model proposed by one of us. These results apply to a large class of theories in which the Hilbert space has a basis of states given by ribbon graphs embedded in a three-dimensional manifold up to diffeomorphisms, and the dynamics is given by local moves on the graphs, such as arise in the representation theory of quantum groups. For such models, matter appears to be already included in the microscopic kinematics and dynamics.Comment: 12 pages, 21 figures, improved presentation, results unchange